Supplementary Materials for · Supplementary Materials: Materials and Methods Candidate biomarkers...
Transcript of Supplementary Materials for · Supplementary Materials: Materials and Methods Candidate biomarkers...
www.sciencetranslationalmedicine.org/cgi/content/full/5/207/207ra142/DC1
Supplementary Materials for
A Blood-Based Proteomic Classifier for the Molecular Characterization of Pulmonary Nodules
Xiao-jun Li,* Clive Hayward, Pui-Yee Fong, Michel Dominguez, Stephen W.
Hunsucker, Lik Wee Lee, Matthew McLean, Scott Law, Heather Butler, Michael Schirm, Olivier Gingras, Julie Lamontagne, Rene Allard, Daniel Chelsky, Nathan D. Price,
Stephen Lam, Pierre P. Massion, Harvey Pass, William N. Rom, Anil Vachani, Kenneth C. Fang, Leroy Hood, Paul Kearney*
*Corresponding author. E-mail: [email protected] (X.-j.L.); [email protected] (P.K.)
Published 16 October 2013, Sci. Transl. Med. 5, 207ra142 (2013)
DOI: 10.1126/scitranslmed.3007013
This PDF file includes:
Materials and Methods Fig. S1. Summary of 388 lung cancer biomarker candidates. Fig. S2. Summary of the 371-protein MRM assay. Fig. S3. ROC curves of the classifier in discovery and validation. Fig. S4. Scatter plot of nodule size versus classifier score of all 247 patients. Fig. S5. Performance of individual proteins as normalizers. Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies. Table S2. Terminologies used for searching potential biomarkers in literature. Table S3. Information of 388 protein candidates. Table S4. Summary of protein MRM assay development and detection in blood. Table S6. Experimental design of the discovery study. Table S7. The list of 36 cooperative proteins. Table S8. Results from logistic regression diagnostics. Table S9. Experimental design of the validation study. Table S10. Impact of clinical characteristics on classifier score. Table S11. List of endogenous normalizing proteins. Table S12. Protein and peptide detection in the discovery study. References (50–71)
Other Supplementary Material for this manuscript includes the following: (available at www.sciencetranslationalmedicine.org/cgi/content/full/5/207/207ra142/DC1)
Table S5 (.pdf format). MRM assay of individual proteins.
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Supplementary Materials:
Materials and Methods
Candidate biomarkers identified by tissue proteomics. Specimens of resected
adenocarcinoma, squamous cell and large cell lung tumors and non-adjacent normal
tissue in the same lobe were obtained from patients who provided informed consent in
studies approved by the Ethics Review Boards at the Centre Hospitalier de l’Université
de Montréal and the McGill University Health Centre.
The proteomic analyses of lung tumor tissues targeted membrane-associated proteins on
endothelial cells (adenocarcinoma, n=13; squamous cell, n=18; and large cell, n=7) and
epithelial cells (adenocarcinoma, n=19; squamous cell, n=6; and large cell, n=5), and
those associated with the Golgi apparatus (adenocarcinoma, n=13; squamous cell, n=15;
and large cell, n=5): See Table S1.
Membrane proteins from endothelial cells or epithelial cells and secreted proteins were
isolated from normal or tumor tissues from fresh lung resections after washing in buffer
and disruption with a Polytron to prepare homogenates. The cell membrane protocol
included filtration using 180 µm mesh and centrifugation at 900 x g for 10 min at 4°C,
supernatants prior to layering on 50% (w:v) sucrose and centrifugation at 218,000 x g for
1 h at 4°C to pellet the membranes. Membrane pellets were resuspended and treated with
micrococcal nuclease, and incubated with the following antibodies specified by plasma
membrane type: endothelial membranes (anti-thrombomodulin, anti-ACE, anti-CD34 and
anti-CD144 antibodies); epithelial membranes (anti-ESA, anti-CEA, anti-CD66c and
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anti-EMA antibodies), prior to centrifugation on top of a 50%(w:v) sucrose cushion at
280,000 x g (endothelial) or 218,000 x g (epithelial) for 1 h at 4°C. After pellet
resuspension, plasma membranes were isolated using MACS microbeads. Endothelial
plasma membranes were treated with KI to remove cytoplasmic peripheral proteins. The
eluate of epithelial plasma membranes was centrifuged at 337,000 x g for 30 min at 4°C
over a 33%(w:v) sucrose cushion, with resuspension of the pellet in Laemmli/Urea/DTT
after removal of the supernatant and sucrose cushion.
To isolate secreted tissue proteins, the density of the tissue homogenates (prepared as
described above) was adjusted to 1.4 M sucrose prior to isolating the secretory vesicles
by isopycnic centrifugation at 100,000 x g for 2 h at 4°C on a 0.8 and 1.2 M
discontinuous sucrose gradient. Vesicles concentrating at the 0.8/1.2 M interface were
collected and further incubated for 25 min with 0.5 M KCl to remove loosely bound
peripheral proteins. Vesicles were recuperated by ultracentrifugation at 150,000 x g for 1
h at 4°C and then opened with 100 mM (NH4)HCO3 (pH 11.0) for 30 min at 4°C.
Secreted proteins were recovered in the supernatant following ultracentrifugation at
150,000 x g for 1 h at 4°C.
Membrane or secreted proteins were then analyzed by CellCarta (Caprion) proteomics
platform, including digestion by trypsin, separation by strong cation exchange
chromatography, and analysis by reversed-phase liquid chromatography coupled with
electrospray tandem mass spectrometry (MS/MS). Peptides in the samples were
identified by database searching of MS/MS spectra using MASCOT (50) and quantified
by a label-free approach based on their signal intensity in the samples, similar to those
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described in the literature (51-53). Proteins whose tumor-to-normal abundance ratio was
either ≥1.5 or ≤2/3 were then identified as candidate biomarkers. The results are provided
in Table S3.
Candidate biomarkers identified by literature searches. Automated literature searches
using predefined terms detailed in Table S2 and automated PERL scripts were performed
on the following databases: UniProt (www.uniprot.org ) on May 6, 2010, Entrez
(www.ncbi.nlm.nih.gov/books/NBK3836) on May 17, 2010, and NextBio
(www.nextbio.com ) on July 8, 2010. Biomarker candidates were compiled and mapped
to UniProt identifiers using the UniProt Knowledge Base
(http://www.uniprot.org/help/uniprotkb). The results are provided in Table S3.
Presence of candidate biomarkers in the blood. The tissue- and literature-identified
biomarker candidates were required to demonstrate documented evidence in the literature
or in a database as a soluble or solubilized circulating protein. The first criterion was
evidence by mass spectrometry detection, with a candidate designated as previously
detected by the following database-specific criteria: a minimum of 2 peptides in
HUPO9504, which contains 9,504 human proteins identified by MS/MS (54); a minimum
of 1 peptide in HUPO889, which is a higher confidence subset of HUPO9504 containing
889 human proteins (55); or at least 2 peptides in Peptide Atlas (56) (November 2009
build). The second criterion was annotation as either a secreted or single-pass membrane
protein in UniProt. The third criterion was designation as a plasma protein in the
literature (57). The fourth criterion was prediction as a secreted protein based on the use
of various programs: prediction by TMHMM (58) as a protein with one transmembrane
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domain, which however is cleaved based on prediction by SignalP (59); or prediction by
TMHMM as having no transmembrane domain and prediction by either SignalP (59) or
SecretomeP (60) as a secreted protein. All candidate proteins satisfied one or more of the
criteria. The results are provided in Table S3.
Sample, subject and lung nodule inclusion and exclusion criteria. The inclusion criteria
for plasma samples were collection in EDTA-containing blood tubes; obtained from
subjects previously enrolled in the Ethics Review Board (ERB) or the Institutional
Review Boards (IRB) approved studies at the participating institutions; and archived, e.g.
labeled, aliquoted and frozen, as stipulated by the study protocols.
The inclusion criteria for subjects were the following: age ≥ 40; any smoking status, e.g.
current, former, or never; any co-morbid conditions, e.g. chronic obstructive pulmonary
disease (COPD); any prior malignancy with a minimum of 5 years in clinical remission;
any prior history of skin carcinomas, e.g. squamous or basal cell. The only exclusion
criterion was prior malignancy within 5 years of lung nodule diagnosis.
The inclusion criteria for the lung nodules included radiologic, histopathologic and
staging parameters. The radiologic criteria included size ≥ 4 mm and ≤ 30 mm, and any
spiculation or ground glass opacity. The histopathologic criteria included either diagnosis
of malignancy, e.g. non-small cell lung cancer (NSCLC), including adenocarcinoma,
bronchioloalveolar carcinoma (BAC), squamous, or large cell, or a benign process,
including inflammatory (e.g. granulomatous, infectious) ornon-inflammatory (e.g.
hamartoma) processes. The clinical staging parameters included: primary tumor: ≤T1
(e.g. 1A and 1B); regional lymph nodes: N0 or N1 only; distant metastasis: M0 only. The
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exclusion criteria for lung nodules included the following: nodule size data unavailable;
no pathology data available, histopathologic diagnosis of small cell lung cancer; and the
following clinical staging parameters: primary tumor: ≥T2, regional lymph nodes: ≥N2,
and distant metastasis: ≥M1.
Sample layout. Up to 15 paired samples per batch were assigned randomly and iteratively
to experimental processing batches until no statistical bias was demonstrable on age,
gender or nodule size. Paired samples within each processing batch were further
randomly and repeatedly assigned to positions within the processing batch until the
absolute values of the corresponding Pearson correlation coefficients between position
and age, gender and nodule size were less than 0.1. Each pair of cancer and benign
samples was then randomized to their relative positions in the batch. To provide a
positive control for quality assessment, three 200 µl aliquots of a pooled human plasma
standard (HPS) (Bioreclamation) were positioned at the beginning, middle and end of
each processing batch, respectively. Samples within a batch were analyzed together:
sequentially during immunodepletion and MRM-MS analysis but in parallel during
denaturing, digestion, and desalting. Details of the sample layouts in the discovery and
the validation study are provided in Tables S6 and S9.
Power analysis for the classifier discovery study. The power analysis for the discovery
study was based on the following assumptions: (A) The overall false positive rate (�) was
set to 0.05. (B) Šidák correction for multiple testing (61) was used to calculate the
effective ���� for testing 200 proteins, i.e. ���� � 1 � √1 � �� . (C) The effective
sample size was reduced by a factor of 0.864 to account for the larger sample requirement
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for the Mann-Whitney test than for the t-test (62). (D) The overall coefficient of variation
was set to 0.43 based on a previous experience. (E) The power (1-β) of the study was
calculated based on the formula (63) for the two-sample, two-sided t-test, using effective
���� and effective sample size.
Power analysis for the classifier validation study. Sufficient cancer and benign samples
were needed in the validation study to confirm the performance of the lung nodule
classifier obtained from the discovery study. We were interested in obtaining the 95%
confidence intervals (CIs) on NPV and specificity for the classifier. Assuming the cancer
prevalence of lung nodules was �� , the negative predictive value (NPV) and the
positive predictive value (PPV) of a classifier on the intended use population with lung
nodules were calculated from sensitivity (����) and specificity (���) as follows:
��� ���������∗����
����∗�����������������∗���� (S1)
��� � ����∗��������∗�������������∗��������
(S2)
Using Eq. (S1) above, we derived sensitivity as a function of NPV and specificity, i.e.
���� � 1 � �� !" !"
����������
��� (S3)
If the validation study contained �# cancer samples and �$ benign samples, variances of
sensitivity and specificity based on binomial distribution were given by (64)
%������� � ���� ∗ �1 � �����/�# (S4)
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%������ � ��� ∗ �1 � ����/�$ (S5)
Using Eqs. (S1, S2) above, the corresponding variances of NPV and PPV were derived
under the large-sample, normal-distribution approximation as (64)
%������ � ���'�1 � ����'(�)�������
���������* �)�������
�����+, (S6)
%������ � ���'�1 � ����'(�)�������
�����* �)�������
���������+. (S7)
The two-sided 95% CIs of sensitivity, specificity, NPV and PPV were then given by
,-��./'/ %�������, ,-��./'/ %������, ,-��./'/ %������ and
,-��./'/ %������, respectively, where -��./' � 1.959964 was the 97.5% quantile of
the normal distribution.
Immunoaffinity chromatography. An immunoaffinity column was prepared by adding 10
ml of a 50% slurry containing a 2:1 ratio of IgY14 and SuperMix resins (Sigma Aldrich),
respectively, to a glass chromatography column (Tricorn, GE Healthcare) and allowed to
settle by gravity, yielding a 5 ml volume of resin in the column. The column was capped
and placed on an HPLC system (Agilent 1100 series) for further packing with 0.15 M
(NH4)HCO3 at 2 ml/min for 20 min, with performance assessed by replicate injections of
HPS aliquots. Column performance was assessed prior to immunoaffinity separation of
each sample batch.
To isolate low abundance proteins, 60 µl of plasma were diluted in 0.15M (NH4)HCO3
(1:2 v/v) to a 180 µl final volume and filtered using a 0.2 µm AcroPrep 96-well filter
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plate (Pall Life Sciences). Immunoaffinity separation was conducted on a IgY14-
SuperMix column connected to an HPLC system (Agilent 1100 series) using 3 buffers
(loading/washing: 0.15 M (NH4)HCO3; stripping/elution: 0.1 M glycine, pH 2.5; and
neutralization: 0.01 M Tris-HCl and 0.15 M NaCl, pH 7.4) with a cycle comprised of
load, wash, elute, neutralization and re-equilibration lasting 36 min. The unbound and
bound fractions were monitored at 280 nm and were baseline resolved after separation.
Unbound fractions (containing the low abundance proteins) were collected for
downstream processing and analysis, and lyophilized prior to enzymatic digestion.
Enzymatic digestion and solid-phase extraction. Lyophilized fractions containing low
abundance proteins were digested with trypsin after being reconstituted under mild
denaturing conditions in 200 µl of 1:1 0.1 M (NH4)HCO3 /trifluoroethanol (TFE) (v/v)
and then allowed to incubate on an orbital shaker for 30 min at RT. Samples were diluted
in 800 µl of 0.1 M (NH4)HCO3 and digested with 0.4 µg trypsin (Princeton Separations)
per sample for 16 h at 37 °C and lyophilized. Lyophilized tryptic peptides were
reconstituted in 350 µl of 0.01 M (NH4)HCO3 and incubated on an orbital shaker for 15
min at RT, followed by reduction using 30 µl of 0.05 M TCEP and incubation for 1 h at
RT and dilution in 375 µl of 90% water/10% acetonitrile/0.2% trifluoroacetic acid. The
extraction plate (Empore C18, 3M Bioanalytical Technologies) was conditioned
according to the manufacturer's protocol, and after sample loading were washed in 500 µl
of 95% water/5% acetonitrile/0.1% trifluroacetic acid and eluted by 200 µl of 52%
water/48% acetonitrile/0.1% trifluoroacetic acid into a collection plate. The eluate was
split into 2 equal aliquots and was taken to dryness in a vacuum concentrator. One aliquot
was used immediately for mass spectrometry, while the other was stored at -80°C.
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Samples were reconstituted in 12 µl of 90% water/10% acetonitrile/0.2% formic acid just
prior to LC-MRM MS analysis.
Development of MRM assays. MRM assays for candidate proteins were developed based
on synthetic peptides (17, 26, 33). After identification and synthesis of up to five suitable
peptides per protein, MRM triggered MS/MS spectra were collected on a 5500 QTrap
mass spectrometer for both doubly and triply charged precursor ions. The obtained
MS/MS spectra were assigned to peptides using MASCOT (50). Since the MS/MS
spectra were collected from the mixture of synthetic peptides, a minimum cutoff score of
15 was used in peptide assignment. Up to four transitions per precursor ion were then
selected for optimization. The resulting corresponding optimal retention time,
declustering potential and collision energy were assembled for all transitions. Optimal
transitions were measured on a mixture of all synthetic peptides and on two pooled
plasma samples, each obtained from ten subjects with either benign or malignant, i.e.
NSCLC, lung nodules at the Institut Universitaire de Cardiologie et de Pneumologie de
Quebec (IUCPQ). All subjects provided informed consent and contributed biospecimens
in studies approved by the institution’s Ethics Review Board (ERB). Plasma samples
were processed as described above. Batches of 1750 transitions were analyzed by MRM-
MS, as described below. The two best transition per peptide and two best peptides per
protein were selected manually. The intensity ratio between the two best transitions of a
peptide in the synthetic peptide mixture, was used to assess the specificity of the
transitions in a biological sample. Transitions demonstrating interference with other
transitions were not selected. A method of calculating q values of peptide and protein
assays was developed to ensure that the observed transitions corresponded to the peptides
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and proteins they were intended to measure, as described below. About 93% of peptide
transitions developed had an error rate below 5%.
MRM-MS analysis. Peptide samples were separated using a capillary reversed-phase LC
column (Thermo BioBasic 18 KAPPA; column dimensions: 320 µm x 150 mm; particle
size: 5 µm; pore size: 300 Å) and a nano-HPLC system (nanoACQUITY, Waters Inc.).
The mobile phases were (A) 0.2% formic acid in water and (B) 0.2% formic acid in
acetonitrile. The samples were injected (8 µl) and separated using a linear gradient (98%
A to 70% A) at 5 µl/minute for 19 min. Peptides were eluted directly into the electrospray
source of the mass spectrometer (5500 QTrap LC/MS/MS, AB Sciex) operating in
scheduled MRM positive-ion mode (Q1 resolution: unit; Q3 resolution: unit; detection
window: 180 seconds; cycle time: 1.5 seconds). Transition intensities were then
integrated by software MultiQuant (AB Sciex). An intensity threshold of 10,000 was used
to filter out non-specific data and undetected transitions.
Calculation of q-values of peptide and protein assays. In the development of MRM
assays, it is important to ensure that the transitions detected correspond to the peptides
and proteins they were intended to measure. Computational tools such as mProphet (65)
enable automated qualification of MRM assays. We introduced a complementary strategy
to mProphet that does not require customization for each dataset. It utilizes expression
correlation techniques (66) to confirm the identity of transitions from the same peptide
and protein with high confidence. In Fig. S2(B), a histogram of the Pearson correlations
between every pair of transitions in the assay is presented. The correlation between a pair
of transitions was obtained from their expression profiles over all samples in the
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discovery study. As expected, transitions from the same peptide were highly correlated.
Similarly, transitions from different peptide fragments of the same protein were also
highly correlated. In contrast, transitions from different proteins were not highly
correlated, which enabled a statistical analysis of the quality of a protein’s MRM assay.
To determine the false positive assay rate we calculated the q-values (67) of peptide
MRM assays. Using the distribution of Pearson correlations between transitions
from different proteins as the null distribution (Fig. S2(B)), an empirical p-value was
assigned to a pair of transitions from the same peptide, detected in at least five
common samples. A value of ‘NA’ was assigned if the pair of transitions were
detected in less than five common samples. The empirical p-value was converted to
a q-value using the “qvalue” package in Bioconductor
(www.bioconductor.org/packages/release/bioc/html/qvalue.html). We calculated
the q-values of protein MRM assays in the same way except Pearson correlations of
individual proteins were calculated as those between two transitions from different
peptides of the protein. For proteins not having two peptides detected in five or
more common samples, their q-values could not be properly evaluated and were
assigned ‘NA’. If the correlation of transitions from two peptides from the same
protein was above 0.5 then there was less than a 3% probability that the assay was
false. See Table S12 for more details.
Definition of depletion column drift. Due to changes in observed signal intensity after
repetitive use of each immunoaffinity column, the column's performance was assessed by
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quantifying the transition intensity in the control HPS samples. Assuming 56,� was the
intensity of transition 8 in an HPS sample �, the drift of the sample was defined as
9�8:;� � <�98%��=>,?�=@?=@?�, (S8)
where 5@6 was the mean value of 56,� among all HPS samples that were depleted by the
same column, and the median was taken over all detected transitions in the sample. The
column variability, or drift, was defined as
9�8:;�AB � <�98%��9�8:;� C 0� � <�98%��9�8:;� E 0�. (S9)
Here the median was taken over all HPS samples depleted by the column. If no sample
drift were greater or less than zero, the corresponding median was taken as 0. The median
column drift was the median of drifts of all depletion columns used in the study.
Calibration by human plasma standard (HPS) samples. For a label-free MS approach,
variation on signal intensity between different experiments is expected. To reduce this
variation, we utilized HPS samples as an external standard and calibrated the intensity
between the discovery and validation studies. Assuming that 5F6,� was the logarithmically
transformed (base 2), normalized intensity of transition 8 in sample �, 5F6,G6� and 5F6,�)B were
the corresponding median values of HPS samples in the discovery and the validation
studies, respectively, then the HPS corrected intensity was
5H6,� � 5I6,� � 5I6,�)B * 5I6,G6� (S10)
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Figures
Fig. S1. Summary of 388 lung cancer biomarker candidates. (A) Venn diagram
of sources of tissue biomarkers (see Table S1). (B) Venn diagram of biomarkers
in literature (see Table S2). (C) Overlap between tissue biomarkers and
biomarkers in literature. (D) Venn diagram of evidences for protein presence in
blood (see Table S3 for details).
7"
87"
32"
66"
4"
32"91"
Lung"cancers"(276)"
Diseases"causing"benign"lung"nodules"
(168)"
Symptoms"of"benign"or"cancerous"lung"nodules"(159)"
Total"number:"319"
Tissue"biomarkers"
(217)"
Biomarkers"in"literature"
(319)"69" 148" 171"
Total"number:"388"
UniProt"(220)"
Total"number:"388"
Literature"(173)"
40"22"42"
40"
13"
18"
10"
22"
34"
24"
10"
30"
16"12"
55"
DetecIon"(214)" PredicIon"(275)"
A B
C D
70"
24"
47"
24"
24"
8"20"
Secreted"(76)"
Cell"surface"epithelial"(138)"
Cell"surface"endothelial"
(99)"
Total"number:"217"
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Fig. S2. Summary of the 371-protein MRM assay. (A) Protein (blue) and peptide
(green) MRM assay development and detection in blood. (B) Histograms of the
Pearson correlations for transitions from the same peptide (blue), from the same
protein (green) and from different proteins (red).
Selected'for'development'
Synthesized'pep4des'
Developed'SRM'assays'
Detected'in'blood'
Protein' 388' 381' 371' 190'
Pep4de' 1730' 1425' 344'
0'
400'
800'
1200'
1600'
2000' Protein' Pep4de'
0'
0.05'
0.1'
0.15'
0.2'
0.25'
F1' F0.8' F0.6' F0.4' F0.2' 0' 0.2' 0.4' 0.6' 0.8' 1'
freq
uency'
Pearson'correla4on'
Same'pep4de' Same'protein' Different'proteins'
A
B
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Fig. S3. Receiver operating characteristic curves of the classifier in discovery
and validation. The corresponding areas under the receiver operating
characteristic curves (AUCs) were 0.82 and 0.60, respectively.
0.1
.2.3
.4.5
.6.7
.8.9
1Se
nsiti
vity
0 .1 .2 .3 .4 .5 .6 .7 .8 .9 11−Specificity
Discovery Validation
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Fig. S4. Scatter plot of nodule size vs. classifier score of all 247 patients. The
plot demonstrated the lack of correlation between the two variables. (A) Samples
in discovery and (B) samples in validation.
Classifier score
Nod
ule
size
(mm
)
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
0
5
10
15
20
25
30
35
40
45 BenignCancer
A
Classifier score
Nod
ule
size
(mm
)
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
0
5
10
15
20
25
30 BenignCancer
B
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Fig. S5. Performance of individual proteins as normalizers. APOA1 was not
selected as a normalizer due to high biological coefficient of variation (CV).
K1C19 was not slected since it is a common contamination in mass spectrometry
analysis.
●
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●
●
●
●
●
0 5 10 15 20
05
1015
20
Rank in reducing technical CV
Ran
k in
redu
cing
col
umn
drift
LG3BP
PEDF
APOA1
MASP1
C163A
LUM
GELS
IBP2
AMPN
PTPRJ
K1C19
ICAM3
IBP3
DSG2
APOE
CD14
COIA1
GGH●
●
●
●
●
●
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Tables
Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies.
Isolation Histologic type Histologic grade
Extent of invasion
Regional lymph nodes
Distant metastasis
Gender
Cell Surface (Endothelial)
adenocarcinoma G1 T2 N0 M0 F
Cell Surface (Endothelial)
adenocarcinoma G2 T1 N0 MX M
Cell Surface (Endothelial)
adenocarcinoma G2 T2 N0 M1 F
Cell Surface (Endothelial)
adenocarcinoma G2 T2 N0 MX M
Cell Surface (Endothelial)
adenocarcinoma G2 T2 N1 MX F
Cell Surface (Endothelial)
adenocarcinoma G2 T2 N2 MX M
Cell Surface (Endothelial)
adenocarcinoma G2 T3 N0 M0 M
Cell Surface (Endothelial)
adenocarcinoma G3 T1 N0 MX M
Cell Surface (Endothelial)
adenocarcinoma G3 T1 N2 MX F
Cell Surface (Endothelial)
adenocarcinoma G3 T2 N0 MX F
Cell Surface (Endothelial)
adenocarcinoma G3 T2 N0 MX M
Cell Surface (Endothelial)
adenocarcinoma G3 T3 N0 MX M
Cell Surface (Endothelial)
adenocarcinoma G4 T1 N0 MX F
Cell Surface (Endothelial)
large cell G3 T2 N0 M0 M
Cell Surface (Endothelial)
large cell G3 T2 N0 MX F
Cell Surface (Endothelial)
large cell G3 T4 N0 MX F
Cell Surface (Endothelial)
large cell G4 T2 N0 MX M
Cell Surface (Endothelial)
large cell G4 T2 N1 MX M
Cell Surface (Endothelial)
large cell G4 T2 N2 MX M
Cell Surface (Endothelial)
large cell G4 T3 N0 MX M
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Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies.
Isolation Histologic type Histologic grade
Extent of invasion
Regional lymph nodes
Distant metastasis
Gender
Cell Surface (Endothelial)
squamous G1 T2 n/a M0 M
Cell Surface (Endothelial)
squamous G2 T2 N0 M0 F
Cell Surface (Endothelial)
squamous G2 T2 N0 M0 M
Cell Surface (Endothelial)
squamous G2 T2 N0 M0 M
Cell Surface (Endothelial)
squamous G2 T2 N0 MX F
Cell Surface (Endothelial)
squamous G2 T2 N0 MX M
Cell Surface (Endothelial)
squamous G2 T2 N0 MX M
Cell Surface (Endothelial)
squamous G2 T2 N1 MX M
Cell Surface (Endothelial)
squamous G2 T2 NX MX M
Cell Surface (Endothelial)
squamous G2 T3 N1 M0 M
Cell Surface (Endothelial)
squamous G3 T2 N0 MX F
Cell Surface (Endothelial)
squamous G3 T2 N0 MX M
Cell Surface (Endothelial)
squamous G3 T2 N1 MX M
Cell Surface (Endothelial)
squamous G3 T2 N2 MX F
Cell Surface (Endothelial)
squamous G3 T2 N2 MX M
Cell Surface (Endothelial)
squamous G3 T3 N0 MX M
Cell Surface (Endothelial)
squamous G3 T3 N0 MX M
Cell Surface (Endothelial)
squamous G3 T3 N1 M0 M
Cell Surface (Epithelial)
adenocarcinoma G1 T2 N0 M0 F
Cell Surface (Epithelial)
adenocarcinoma G2 T1 N0 MX M
Cell Surface (Epithelial)
adenocarcinoma G2 T1 N0 MX M
Submitted Manuscript: Confidential
20
Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies.
Isolation Histologic type Histologic grade
Extent of invasion
Regional lymph nodes
Distant metastasis
Gender
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N0 M1 F
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N0 MX F
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N0 MX M
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N1 MX F
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N2 MX M
Cell Surface (Epithelial)
adenocarcinoma G2 T2 N2 MX M
Cell Surface (Epithelial)
adenocarcinoma G2 T2 NX MX M
Cell Surface (Epithelial)
adenocarcinoma G2 T4 N2 MX F
Cell Surface (Epithelial)
adenocarcinoma G2/3 T1 N0 M0 M
Cell Surface (Epithelial)
adenocarcinoma G2/3 T1 N1 MX M
Cell Surface (Epithelial)
adenocarcinoma G3 T1 N0 MX F
Cell Surface (Epithelial)
adenocarcinoma G3 T1 N2 MX F
Cell Surface (Epithelial)
adenocarcinoma G3 T2 N0 MX F
Cell Surface (Epithelial)
adenocarcinoma G3 T2 N0 MX M
Cell Surface (Epithelial)
adenocarcinoma G3 T2 N0 MX M
Cell Surface (Epithelial)
adenocarcinoma G3 T2 N0 MX n/a
Cell Surface (Epithelial)
large cell G3 T1 N0 MX F
Cell Surface (Epithelial)
large cell G3 T2 N0 M0 F
Cell Surface (Epithelial)
large cell G3 T2 N0 MX F
Cell Surface (Epithelial)
large cell G4 T2 N0 MX M
Cell Surface (Epithelial)
large cell G4 T2 N2 MX M
Submitted Manuscript: Confidential
21
Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies.
Isolation Histologic type Histologic grade
Extent of invasion
Regional lymph nodes
Distant metastasis
Gender
Cell Surface (Epithelial)
squamous G1 T4 N1 MX M
Cell Surface (Epithelial)
squamous G2 T2 N0 M0 F
Cell Surface (Epithelial)
squamous G2 T2 N0 M0 M
Cell Surface (Epithelial)
squamous G2 T2 N0 MX M
Cell Surface (Epithelial)
squamous G3 T2 N0 MX F
Cell Surface (Epithelial)
squamous G3 T2 N1 MX M
Secreted adenocarcinoma G1 T2 n/a MX F Secreted adenocarcinoma G1 T2 N0 M0 F Secreted adenocarcinoma G2 T1 N0 MX F Secreted adenocarcinoma G2 T1 N0 MX M Secreted adenocarcinoma G2 T1 N1 MX F Secreted adenocarcinoma G2 T2 N0 M1 F Secreted adenocarcinoma G2 T2 N2 MX M Secreted adenocarcinoma G2 T3 N0 M0 M Secreted adenocarcinoma G2/3 T1 N0 M0 M Secreted adenocarcinoma G3 T1 N1 MX F Secreted adenocarcinoma G3 T1 N2 MX F Secreted adenocarcinoma G3 T2 N0 MX F Secreted adenocarcinoma G3 T2 N0 MX M Secreted large cell G3 T2 N0 M0 M Secreted large cell G3 T2 N0 MX F Secreted large cell G3 T3 N1 MX F Secreted large cell G4 T2 N0 MX M Secreted large cell G4 T2 N2 MX M Secreted squamous G1 T1 N0 MX F Secreted squamous G1 T2 N1 M0 M Secreted squamous G1 T2 NX M0 M Secreted squamous G2 T1 N1 M0 F Secreted squamous G2 T2 N0 M0 F Secreted squamous G2 T2 N0 M0 M Secreted squamous G2 T2 N0 MX M Secreted squamous G2 T2 N0 MX M Secreted squamous G3 T1 N0 MX F Secreted squamous G3 T2 N0 MX M Secreted squamous G3 T2 N1 MX M Secreted squamous G3 T2 N1 MX M Secreted squamous G3 T2 N1 MX M
Submitted Manuscript: Confidential
22
Table S1. Clinical information of lung cancer patients enrolled in tissue biomarker studies.
Isolation Histologic type Histologic grade
Extent of invasion
Regional lymph nodes
Distant metastasis
Gender
Secreted squamous G3 T3 N0 MX M Secreted squamous G3 T3 N1 M0 M
Note:
• Histologic grade o G1 = Well differentiated. o G2 = Moderately differentiated. o G3 = Poorly differentiated. o G4 = Undifferentiated.
• Extent of invasion o T1 = Tumor ≤ 3 cm in greatest dimension, surrounded by lung or visceral
pleura, without bronchoscopic evidence of invasion more proximal than the lobar bronchus.
o T2 = Tumor with any of the following features of size or extent: > 3 cm in greatest dimension, involves main bronchus, ≥ 2 cm distal to the carina, invades the visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
o T3=Tumor of any size that directly invades any of the following Chest wall (including superior sulcus tumors), diaphragm, mediastinial pleura or parietal pericardium.
o T4 = Tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, esophagus, vertebral body, carina.
• Regional lymph nodes o NX = Cannot be assessed. N0 = No regional lymph node metastasis. o N1 = Metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph
nodes, including intrapulmonary nodes involved by direct extension of the primary tumor.
o N2 = Metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). o n/a = not available.
• Distant metastasis o MX = Cannot be assessed. o M0 = No distant metastasis. o M1 = Distant metastasis, includes separate tumor nodule(s) in a different lobe
(ipsilateral or contralateral). • Gender
o F = Female o M = Male
Submitted Manuscript: Confidential
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Table S2. Terminologies used for searching potential biomarkers in literature.
Lung cancer Disease causing benign
lung nodules
Symptom of cancerous
or benign lung nodules
Bronchial adenoma
Bronchioalveolar
carcinoma
Bronchioloalveolar
carcinoma
Bronchogenic carcinoma
Large cell lung cancer
Large cell lung carcinoma
Lung adenocarcinoma
Lung cancer
Lung carcinoid
Lung carcinoma
Lung carcinosarcoma
Lung chondrosarcoma
Lung lymphoma
Lung mesothelioma
Lung pleomorphic
carcinoma
Lung rhabdomysarcoma
Lung sarcoma
Lung solitary fibrous
tumor
Nonsmall cell lung cancer
Non-small cell lung
cancer
Nonsquamous cell lung
carcinoma
Non-small cell lung
cancer
Nonsquamous cell lung
carcinoma
Non-squamous cell lung
carcinoma
NSCLC
Pleura solitary fibrous
tumor
Pulmonary
adenocarcinoma
Anthracosilicosis
Asbestosis
Atelectasis
Bronchiectasis
Bronchitis
Bronchogenic cyst
Caplan's disease
Caplan's syndrome
Castleman's disease
Chronic obstructive
pulmonary disease
Cystic fibrosis
Emphysema
Eosinophilic granuloma
Fibrosing alveolitis
Hemangioma
Lung abscess
Lung actinomycosis
Lung amyloidosis
Lung arteriovenous
malformation
Lung aspergilloma
Lung aspergillosis
Lung blastoma
Lung blastomycosis
Lung coccidioidomycosis
Lung consolidation
Lung cryptococcosis
Lung cyst
Lung dirofilariasis
Lung embolism
Lung fibroma
Lung fibrosis
Lung granuloma
Lung hamartoma
Lung histoplasmosis
Lung hyalinizing
Alkaline phosphatase
Anemia
Hemoptysis
Liver enzyme
Serum calcium
Submitted Manuscript: Confidential
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Table S2. Terminologies used for searching potential biomarkers in literature.
Lung cancer Disease causing benign
lung nodules
Symptom of cancerous
or benign lung nodules
Pulmonary cancer
Pulmonary carcinoid
Pulmonary carcinoma
Pulmonary
carcinosarcoma
Pulmonary
chondrosarcoma
Pulmonary lymphoma
Pulmonary
mesothelioma
Pulmonary pleomorphic
carcinoma
Pulmonary
rhabdomysarcoma
Pulmonary sarcoma
Pulmonary solitary
fibrous tumor
SCLC
Small cell lung cancer
Squamous cell lung
carcinoma
granuloma
Lung infarct
Lung infarction
Lung infection
Lung mycosis
Lung neurofibroma
Lung nocardiosis
Lung rheumatoid arthritis
Lung Sarcoidosis
Lung sequestration
Lung toxocariasis
Lung veno-occlusive
disease
Lung Wegener
granulomatosis
Lymph node hyperplasia
Pneumocystosis
Pneumonia
Pulmonary abscess
Pulmonary actinomycosis
Pulmonary amyloidosis
Pulmonary arteriovenous
malformation
Pulmonary aspergilloma
Pulmonary aspergillosis
Pulmonary blastoma
Pulmonary blastomycosis
Pulmonary
coccidioidomycosis
Pulmonary consolidation
Pulmonary
cryptococcosis
Pulmonary cyst
Pulmonary dirofilariasis
Pulmonary embolism
Pulmonary fibroma
Pulmonary fibrosis
Pulmonary granuloma
Pulmonary hamartoma
Pulmonary
Submitted Manuscript: Confidential
25
Table S2. Terminologies used for searching potential biomarkers in literature.
Lung cancer Disease causing benign
lung nodules
Symptom of cancerous
or benign lung nodules
histoplasmosis
Pulmonary hyalinizing
granuloma
Pulmonary infarct
Pulmonary infarction
Pulmonary infection
Pulmonary mycosis
Pulmonary neurofibroma
Pulmonary nocardiosis
Pulmonary rheumatoid
arthritis
Pulmonary Sarcoidosis
Pulmonary sequestration
Pulmonary toxocariasis
Pulmonary veno-
occlusive disease
Pulmonary Wegener
granulomatosis
Rheumatoid lung disease
Tuberculosis
Submitted Manuscript: Confidential
26
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
1433B 14-3-3 protein beta/alpha YWHAB Secreted, EPI LungCancers Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection
1433E 14-3-3 protein epsilon YWHAE ENDO LungCancers, BenignNodules
Cytoplasm (By similarity). Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection
1433S 14-3-3 protein sigma SFN Secreted, EPI LungCancers Cytoplasm. Nucleus (By similarity). Secreted. Note=May be secreted by a non-classical secretory pathway.
UniProt, Literature, Detection
1433T 14-3-3 protein theta YWHAQ EPI LungCancers, BenignNodules
Cytoplasm. Note=In neurons, axonally transported to the nerve terminals.
Detection
1433Z 14-3-3 protein zeta/delta YWHAZ EPI LungCancers, BenignNodules
Cytoplasm. Melanosome. Note=Located to stage I to stage IV melanosomes.
Detection
6PGD 6-phosphogluconate dehydrogenase, decarboxylating
PGD EPI, ENDO Cytoplasm (By similarity). Detection
A1AG1 Alpha-1-acid glycoprotein 1 ORM1 EPI Symptoms Secreted. UniProt, Literature, Detection, Prediction
ABCD1 ATP-binding cassette sub-family D member 1
ABCD1 ENDO Peroxisome membrane; Multi-pass membrane protein.
Detection, Prediction
ADA12 Disintegrin and metalloproteinase domain-containing protein 12
ADAM12 LungCancers, BenignNodules, Symptoms
Isoform 1: Cell membrane; Single-pass type I membrane protein.|Isoform 2: Secreted.|Isoform 3: Secreted (Potential).|Isoform 4: Secreted (Potential).
UniProt, Detection, Prediction
ADML ADM ADM LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
AGR2 Anterior gradient protein 2 homolog
AGR2 EPI LungCancers Secreted. Endoplasmic reticulum (By similarity).
UniProt, Prediction
AIFM1 Apoptosis-inducing factor 1, mitochondrial
AIFM1 EPI, ENDO LungCancers Mitochondrion intermembrane space. Nucleus. Note=Translocated to the nucleus upon induction of apoptosis.
Detection, Prediction
ALDOA Fructose-bisphosphate aldolase A
ALDOA Secreted, EPI LungCancers, Symptoms
Literature, Detection
AMPN Aminopeptidase N ANPEP EPI, ENDO LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type II membrane protein. Cytoplasm, cytosol (Potential). Note=A soluble form has also been detected.
UniProt, Detection
ANGP1 Angiopoietin-1 ANGPT1 LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
ANGP2 Angiopoietin-2 ANGPT2 LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
APOA1 Apolipoprotein A-I APOA1 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
APOE Apolipoprotein E APOE EPI, ENDO LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
ASM3B Acid sphingomyelinase-like phosphodiesterase 3b
SMPDL3B EPI, ENDO Secreted (By similarity). UniProt, Prediction
AT2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
ATP2A2 EPI, ENDO LungCancers, BenignNodules
Endoplasmic reticulum membrane; Multi-pass membrane protein. Sarcoplasmic reticulum membrane; Multi-pass membrane protein.
Detection
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
ATS1 A disintegrin and metalloproteinase with thrombospondin motifs 1
ADAMTS1 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Literature, Prediction
ATS12 A disintegrin and metalloproteinase with thrombospondin motifs 12
ADAMTS12 LungCancers Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Detection, Prediction
ATS19 A disintegrin and metalloproteinase with thrombospondin motifs 19
ADAMTS19 LungCancers Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Prediction
BAGE1 B melanoma antigen 1 BAGE LungCancers Secreted (Potential). UniProt, Prediction
BAGE2 B melanoma antigen 2 BAGE2 LungCancers Secreted (Potential). UniProt, Prediction
BAGE3 B melanoma antigen 3 BAGE3 LungCancers Secreted (Potential). UniProt, Prediction
BAGE4 B melanoma antigen 4 BAGE4 LungCancers Secreted (Potential). UniProt, Prediction
BAGE5 B melanoma antigen 5 BAGE5 LungCancers Secreted (Potential). UniProt, Prediction
BASP1 Brain acid soluble protein 1 BASP1 Secreted, EPI Cell membrane; Lipid-anchor. Cell projection, growth cone. Note=Associated with the membranes of growth cones that form the tips of elongating axons.
Detection
BAX Apoptosis regulator BAX BAX EPI LungCancers, BenignNodules
Isoform Alpha: Mitochondrion membrane; Single-pass membrane protein. Cytoplasm. Note=Colocalizes with 14- 3-3 proteins in the cytoplasm. Under stress conditions, redistributes to the mitochondrion membrane through the release from JNK-phosphorylated 14-3-3 proteins.|Isoform Beta: Cytoplasm.|Isoform Gamma: Cytoplasm.|Isoform Delta: Cytoplasm (Potential).
UniProt, Literature, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
BDNF Brain-derived neurotrophic factor
BDNF BenignNodules, Symptoms
Secreted. UniProt, Literature, Prediction
BGH3 Transforming growth factor-beta-induced protein ig-h3
TGFBI LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix. Note=May be associated both with microfibrils and with the cell surface.
UniProt, Detection
BMP2 Bone morphogenetic protein 2 BMP2 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature
BST1 ADP-ribosyl cyclase 2 BST1 EPI Symptoms Cell membrane; Lipid-anchor, GPI-anchor. Detection, Prediction
C163A Scavenger receptor cysteine-rich type 1 protein M130
CD163 EPI Symptoms Soluble CD163: Secreted.|Cell membrane; Single-pass type I membrane protein. Note=Isoform 1 and isoform 2 show a lower surface expression when expressed in cells.
UniProt, Detection
C4BPA C4b-binding protein alpha chain
C4BPA LungCancers, Symptoms
Secreted. UniProt, Detection, Prediction
CAH9 Carbonic anhydrase 9 CA9 LungCancers, BenignNodules, Symptoms
Nucleus. Nucleus, nucleolus. Cell membrane; Single-pass type I membrane protein. Cell projection, microvillus membrane; Single-pass type I membrane protein. Note=Found on the surface microvilli and in the nucleus, particularly in nucleolus.
UniProt
CALR Calreticulin CALR EPI Symptoms Endoplasmic reticulum lumen. Cytoplasm, cytosol. Secreted, extracellular space, extracellular matrix. Cell surface. Note=Also found in cell surface (T cells), cytosol and extracellular matrix. Associated with the lytic granules in the cytolytic T-lymphocytes.
UniProt, Literature, Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
CALU Calumenin CALU EPI Symptoms Endoplasmic reticulum lumen. Secreted. Melanosome. Sarcoplasmic reticulum lumen (By similarity). Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
UniProt, Detection, Prediction
CALX Calnexin CANX Secreted, EPI, ENDO
BenignNodules Endoplasmic reticulum membrane; Single-pass type I membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
UniProt, Literature, Detection
CAP7 Azurocidin AZU1 EPI Symptoms Cytoplasmic granule. Note=Cytoplasmic granules of neutrophils.
Prediction
CATB Cathepsin B CTSB Secreted LungCancers Lysosome. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection, Prediction
CATG Cathepsin G CTSG Secreted, ENDO
BenignNodules Cell surface. Detection, Prediction
CBPB2 Carboxypeptidase B2 CPB2 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Detection, Prediction
CCL22 C-C motif chemokine 22 CCL22 LungCancers, BenignNodules
Secreted. UniProt, Prediction
CD14 Monocyte differentiation antigen CD14
CD14 EPI LungCancers, BenignNodules, Symptoms
Cell membrane; Lipid-anchor, GPI-anchor. Literature, Detection, Prediction
CD24 Signal transducer CD24 CD24 LungCancers, BenignNodules
Cell membrane; Lipid-anchor, GPI-anchor. Literature
CD2A2 Cyclin-dependent kinase inhibitor 2A, isoform 4
CDKN2A LungCancers, BenignNodules
Cytoplasm. Nucleus.|Nucleus, nucleolus (By similarity).
Literature, Prediction
CD38 ADP-ribosyl cyclase 1 CD38 EPI, ENDO Symptoms Membrane; Single-pass type II membrane protein.
UniProt, Literature
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
CD40L CD40 ligand CD40LG LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type II membrane protein.|CD40 ligand, soluble form: Secreted.
UniProt, Literature
CD44 CD44 antigen CD44 EPI LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection, Prediction
CD59 CD59 glycoprotein CD59 LungCancers, BenignNodules, Symptoms
Cell membrane; Lipid-anchor, GPI-anchor. Secreted. Note=Soluble form found in a number of tissues.
UniProt, Literature, Detection, Prediction
CD97 CD97 antigen CD97 EPI, ENDO Symptoms Cell membrane; Multi-pass membrane protein.|CD97 antigen subunit alpha: Secreted, extracellular space.
UniProt
CDCP1 CUB domain-containing protein 1
CDCP1 LungCancers Isoform 1: Cell membrane; Single-pass membrane protein (Potential). Note=Shedding may also lead to a soluble peptide.|Isoform 3: Secreted.
UniProt, Prediction
CDK4 Cell division protein kinase 4 CDK4 LungCancers, Symptoms
Literature
CEAM5 Carcinoembryonic antigen-related cell adhesion molecule 5
CEACAM5 EPI LungCancers, BenignNodules, Symptoms
Cell membrane; Lipid-anchor, GPI-anchor. Literature, Prediction
CEAM8 Carcinoembryonic antigen-related cell adhesion molecule 8
CEACAM8 EPI LungCancers Cell membrane; Lipid-anchor, GPI-anchor. Detection, Prediction
CERU Ceruloplasmin CP EPI LungCancers, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
CH10 10 kDa heat shock protein, mitochondrial
HSPE1 ENDO LungCancers Mitochondrion matrix. Literature, Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
CH60 60 kDa heat shock protein, mitochondrial
HSPD1 Secreted, EPI, ENDO
LungCancers, Symptoms
Mitochondrion matrix. Literature, Detection
CKAP4 Cytoskeleton-associated protein 4
CKAP4 EPI, ENDO LungCancers Endoplasmic reticulum-Golgi intermediate compartment membrane; Single-pass membrane protein (Potential).
UniProt
CL041 Uncharacterized protein C12orf41
C12orf41 ENDO Prediction
CLCA1 Calcium-activated chloride channel regulator 1
CLCA1 LungCancers, BenignNodules
Secreted, extracellular space. Cell membrane; Peripheral membrane protein; Extracellular side. Note=Protein that remains attached to the plasma membrane appeared to be predominantly localized to microvilli.
UniProt, Prediction
CLIC1 Chloride intracellular channel protein 1
CLIC1 EPI Nucleus. Nucleus membrane; Single-pass membrane protein (Probable). Cytoplasm. Cell membrane; Single-pass membrane protein (Probable). Note=Mostly in the nucleus including in the nuclear membrane. Small amount in the cytoplasm and the plasma membrane. Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain.
UniProt, Literature, Detection
CLUS Clusterin CLU EPI, ENDO LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
CMGA Chromogranin-A CHGA LungCancers, BenignNodules
Secreted. Note=Neuroendocrine and endocrine secretory granules.
UniProt, Literature, Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
CNTN1 Contactin-1 CNTN1 LungCancers Isoform 1: Cell membrane; Lipid-anchor, GPI- anchor; Extracellular side.|Isoform 2: Cell membrane; Lipid-anchor, GPI- anchor; Extracellular side.
Detection, Prediction
CO4A1 Collagen alpha-1(IV) chain COL4A1 LungCancers Secreted, extracellular space, extracellular matrix, basement membrane.
UniProt, Detection, Prediction
CO5A2 Collagen alpha-2(V) chain COL5A2 LungCancers Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Detection, Prediction
CO6A3 Collagen alpha-3(VI) chain COL6A3 Secreted Symptoms Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Detection, Prediction
COCA1 Collagen alpha-1(XII) chain COL12A1 ENDO LungCancers, Symptoms
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Prediction
COF1 Cofilin-1 CFL1 Secreted, EPI LungCancers, BenignNodules
Nucleus matrix. Cytoplasm, cytoskeleton. Note=Almost completely in nucleus in cells exposed to heat shock or 10% dimethyl sulfoxide.
Detection, Prediction
COIA1 Collagen alpha-1(XVIII) chain COL18A1 LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Literature, Detection, Prediction
COX5A Cytochrome c oxidase subunit 5A, mitochondrial
COX5A Secreted, ENDO
Mitochondrion inner membrane. Prediction
CRP C-reactive protein CRP LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
CS051 UPF0470 protein C19orf51 C19orf51 ENDO Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
CSF1 Macrophage colony-stimulating factor 1
CSF1 LungCancers, BenignNodules
Cell membrane; Single-pass membrane protein (By similarity).|Processed macrophage colony-stimulating factor 1: Secreted, extracellular space (By similarity).
UniProt, Literature, Detection
CSF2 Granulocyte-macrophage colony-stimulating factor
CSF2 LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
CT085 Uncharacterized protein C20orf85
C20orf85 LungCancers, BenignNodules
Prediction
CTGF Connective tissue growth factor CTGF LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix (By similarity). Secreted (By similarity).
UniProt, Literature, Detection, Prediction
CYR61 Protein CYR61 CYR61 LungCancers, BenignNodules
Secreted. UniProt, Prediction
CYTA Cystatin-A CSTA LungCancers Cytoplasm. Literature, Detection
CYTB Cystatin-B CSTB Secreted Cytoplasm. Nucleus. Literature, Detection
DDX17 Probable ATP-dependent RNA helicase DDX17
DDX17 ENDO LungCancers, BenignNodules
Nucleus. Detection, Prediction
DEFB1 Beta-defensin 1 DEFB1 LungCancers, BenignNodules
Secreted. UniProt, Prediction
DESP Desmoplakin DSP EPI, ENDO LungCancers Cell junction, desmosome. Cytoplasm, cytoskeleton. Note=Innermost portion of the desmosomal plaque.
Detection
DFB4A Beta-defensin 4A DEFB4A LungCancers, BenignNodules
Secreted. UniProt
DHI1L Hydroxysteroid 11-beta-dehydrogenase 1-like protein
HSD11B1L LungCancers Secreted (Potential). UniProt, Prediction
Submitted Manuscript: Confidential
35
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
DMBT1 Deleted in malignant brain tumors 1 protein
DMBT1 LungCancers, BenignNodules
Secreted (By similarity). Note=Some isoforms may be membrane-bound. Localized to the lumenal aspect of crypt cells in the small intestine. In the colon, seen in the lumenal aspect of surface epithelial cells. Formed in the ducts of von Ebner gland, and released into the fluid bathing the taste buds contained in the taste papillae (By similarity).
UniProt, Detection, Prediction
DMKN Dermokine DMKN LungCancers Secreted. UniProt, Detection, Prediction
DPP4 Dipeptidyl peptidase 4 DPP4 EPI LungCancers, BenignNodules, Symptoms
Dipeptidyl peptidase 4 soluble form: Secreted.|Cell membrane; Single-pass type II membrane protein.
UniProt, Detection
DSG2 Desmoglein-2 DSG2 ENDO Symptoms Cell membrane; Single-pass type I membrane protein. Cell junction, desmosome.
UniProt, Detection
DX39A ATP-dependent RNA helicase DDX39A
DDX39A EPI Nucleus (By similarity). Prediction
DX39B Spliceosome RNA helicase DDX39B
DDX39B EPI Nucleus. Nucleus speckle. Prediction
DYRK2 Dual specificity tyrosine-phosphorylation-regulated kinase 2
DYRK2 ENDO LungCancers Cytoplasm. Nucleus. Note=Translocates into the nucleus following DNA damage.
Literature
EDN2 Endothelin-2 EDN2 LungCancers Secreted. UniProt, Prediction
EF1A1 Elongation factor 1-alpha 1 EEF1A1 Secreted, EPI LungCancers, BenignNodules
Cytoplasm. Detection
EF1D Elongation factor 1-delta EEF1D Secreted, EPI LungCancers Prediction EF2 Elongation factor 2 EEF2 Secreted, EPI Cytoplasm. Literature,
Detection
Submitted Manuscript: Confidential
36
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
EGF Pro-epidermal growth factor EGF LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature
EGFL6 Epidermal growth factor-like protein 6
EGFL6 LungCancers Secreted, extracellular space, extracellular matrix, basement membrane (By similarity).
UniProt, Detection, Prediction
ENOA Alpha-enolase ENO1 Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Cytoplasm. Cell membrane. Cytoplasm, myofibril, sarcomere, M-band. Note=Can translocate to the plasma membrane in either the homodimeric (alpha/alpha) or heterodimeric (alpha/gamma) form. ENO1 is localized to the M-band.|Isoform MBP-1: Nucleus.
Literature, Detection, Prediction
ENOG Gamma-enolase ENO2 EPI LungCancers, Symptoms
Cytoplasm (By similarity). Cell membrane (By similarity). Note=Can translocate to the plasma membrane in either the homodimeric (alpha/alpha) or heterodimeric (alpha/gamma) form (By similarity).
Literature, Detection, Prediction
ENOX2 Ecto-NOX disulfide-thiol exchanger 2
ENOX2 LungCancers Cell membrane. Secreted, extracellular space. Note=Extracellular and plasma membrane-associated.
UniProt, Detection
ENPL Endoplasmin HSP90B1 Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Endoplasmic reticulum lumen. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection, Prediction
EPHB6 Ephrin type-B receptor 6 EPHB6 LungCancers Membrane; Single-pass type I membrane protein.|Isoform 3: Secreted (Probable).
UniProt, Literature
EPOR Erythropoietin receptor EPOR LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type I membrane protein.|Isoform EPOR-S: Secreted. Note=Secreted and located to the cell surface.
UniProt, Literature, Detection
Submitted Manuscript: Confidential
37
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
ERBB3 Receptor tyrosine-protein kinase erbB-3
ERBB3 LungCancers, BenignNodules
Isoform 1: Cell membrane; Single-pass type I membrane protein.|Isoform 2: Secreted.
UniProt, Literature, Prediction
EREG Proepiregulin EREG LungCancers Epiregulin: Secreted, extracellular space.|Proepiregulin: Cell membrane; Single-pass type I membrane protein.
UniProt
ERO1A ERO1-like protein alpha ERO1L Secreted, EPI, ENDO
Symptoms Endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side. Note=The association with ERP44 is essential for its retention in the endoplasmic reticulum.
Prediction
ESM1 Endothelial cell-specific molecule 1
ESM1 LungCancers, BenignNodules
Secreted. UniProt, Prediction
EZRI Ezrin EZR Secreted LungCancers, BenignNodules
Apical cell membrane; Peripheral membrane protein; Cytoplasmic side. Cell projection. Cell projection, microvillus membrane; Peripheral membrane protein; Cytoplasmic side. Cell projection, ruffle membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm, cell cortex. Cytoplasm, cytoskeleton. Note=Localization to the apical membrane of parietal cells depends on the interaction with MPP5. Localizes to cell extensions and peripheral processes of astrocytes (By similarity). Microvillar peripheral membrane protein (cytoplasmic side).
Literature, Detection, Prediction
F10A1 Hsc70-interacting protein ST13 EPI Cytoplasm (By similarity).|Cytoplasm (Probable).
Detection, Prediction
FAM3C Protein FAM3C FAM3C EPI, ENDO Secreted (Potential). UniProt, Detection
Submitted Manuscript: Confidential
38
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
FAS Fatty acid synthase FASN EPI LungCancers, BenignNodules, Symptoms
Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection
FCGR1 High affinity immunoglobulin gamma Fc receptor I
FCGR1A EPI LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type I membrane protein. Note=Stabilized at the cell membrane through interaction with FCER1G.
UniProt
FGF10 Fibroblast growth factor 10 FGF10 LungCancers Secreted (Potential). UniProt, Prediction
FGF2 Heparin-binding growth factor 2
FGF2 LungCancers, BenignNodules, Symptoms
Literature
FGF7 Keratinocyte growth factor FGF7 LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
FGF9 Glia-activating factor FGF9 LungCancers Secreted. UniProt, Literature, Prediction
FGFR2 Fibroblast growth factor receptor 2
FGFR2 LungCancers, BenignNodules
Cell membrane; Single-pass type I membrane protein.|Isoform 14: Secreted.|Isoform 19: Secreted.
UniProt, Literature, Prediction
FGFR3 Fibroblast growth factor receptor 3
FGFR3 LungCancers Membrane; Single-pass type I membrane protein.
UniProt, Literature, Prediction
FGL2 Fibroleukin FGL2 BenignNodules, Symptoms
Secreted. UniProt, Detection, Prediction
FHIT Bis(5'-adenosyl)-triphosphatase FHIT LungCancers, BenignNodules, Symptoms
Cytoplasm. Literature
Submitted Manuscript: Confidential
39
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
FIBA Fibrinogen alpha chain FGA LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
FINC Fibronectin FN1 Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix.
UniProt, Literature, Detection, Prediction
FKB11 Peptidyl-prolyl cis-trans isomerase FKBP11
FKBP11 EPI, ENDO Membrane; Single-pass membrane protein (Potential).
UniProt, Prediction
FOLH1 Glutamate carboxypeptidase 2 FOLH1 ENDO LungCancers, Symptoms
Cell membrane; Single-pass type II membrane protein.|Isoform PSMA': Cytoplasm.
UniProt, Literature
FOLR1 Folate receptor alpha FOLR1 LungCancers Cell membrane; Lipid-anchor, GPI-anchor. Secreted (Probable).
UniProt
FOXA2 Hepatocyte nuclear factor 3-beta
FOXA2 LungCancers Nucleus. Detection, Prediction
FP100 Fanconi anemia-associated protein of 100 kDa
C17orf70 ENDO Symptoms Nucleus. Prediction
FRIH Ferritin heavy chain FTH1 EPI LungCancers, BenignNodules
Literature, Detection, Prediction
FRIL Ferritin light chain FTL Secreted, EPI, ENDO
BenignNodules, Symptoms
Literature, Detection
G3P Glyceraldehyde-3-phosphate dehydrogenase
GAPDH Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Cytoplasm. Cytoplasm, perinuclear region. Membrane. Note=Postnuclear and Perinuclear regions.
Detection
G6PD Glucose-6-phosphate 1-dehydrogenase
G6PD Secreted, EPI LungCancers, Symptoms
Literature, Detection
G6PI Glucose-6-phosphate isomerase GPI Secreted, EPI Symptoms Cytoplasm. Secreted. UniProt, Literature, Detection
Submitted Manuscript: Confidential
40
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
GA2L1 GAS2-like protein 1 GAS2L1 ENDO Cytoplasm, cytoskeleton (Probable). Prediction GALT2 Polypeptide N-
acetylgalactosaminyltransferase 2
GALNT2 EPI, ENDO Golgi apparatus, Golgi stack membrane; Single-pass type II membrane protein. Secreted. Note=Resides preferentially in the trans and medial parts of the Golgi stack. A secreted form also exists.
UniProt, Detection
GAS6 Growth arrest-specific protein 6 GAS6 LungCancers Secreted. UniProt, Detection, Prediction
GDIR2 Rho GDP-dissociation inhibitor 2
ARHGDIB EPI Cytoplasm. Detection
GELS Gelsolin GSN LungCancers, BenignNodules
Isoform 2: Cytoplasm, cytoskeleton.|Isoform 1: Secreted.
UniProt, Literature, Detection, Prediction
GGH Gamma-glutamyl hydrolase GGH LungCancers Secreted, extracellular space. Lysosome. Melanosome. Note=While its intracellular location is primarily the lysosome, most of the enzyme activity is secreted. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
UniProt, Detection, Prediction
GPC3 Glypican-3 GPC3 LungCancers, Symptoms
Cell membrane; Lipid-anchor, GPI-anchor; Extracellular side (By similarity).|Secreted glypican-3: Secreted, extracellular space (By similarity).
UniProt, Literature, Prediction
GRAN Grancalcin GCA EPI Cytoplasm. Cytoplasmic granule membrane; Peripheral membrane protein; Cytoplasmic side. Note=Primarily cytosolic in the absence of calcium or magnesium ions. Relocates to granules and other membranes in response to elevated calcium and magnesium levels.
Prediction
Submitted Manuscript: Confidential
41
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
GREB1 Protein GREB1 GREB1 ENDO Membrane; Single-pass membrane protein (Potential).
UniProt, Prediction
GREM1 Gremlin-1 GREM1 LungCancers, BenignNodules
Secreted (Probable). UniProt, Prediction
GRP Gastrin-releasing peptide GRP LungCancers, Symptoms
Secreted. UniProt, Prediction
GRP78 78 kDa glucose-regulated protein
HSPA5 Secreted, EPI, ENDO
LungCancers, BenignNodules
Endoplasmic reticulum lumen. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
GSLG1 Golgi apparatus protein 1 GLG1 EPI, ENDO BenignNodules Golgi apparatus membrane; Single-pass type I membrane protein.
UniProt
GSTP1 Glutathione S-transferase P GSTP1 Secreted LungCancers, BenignNodules, Symptoms
Literature, Detection, Prediction
GTR1 Solute carrier family 2, facilitated glucose transporter member 1
SLC2A1 EPI, ENDO LungCancers, BenignNodules, Symptoms
Cell membrane; Multi-pass membrane protein (By similarity). Melanosome. Note=Localizes primarily at the cell surface (By similarity). Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature
GTR3 Solute carrier family 2, facilitated glucose transporter member 3
SLC2A3 EPI Membrane; Multi-pass membrane protein. Detection
H2A1 Histone H2A type 1 HIST1H2AG Secreted Nucleus. Detection, Prediction
H2A1B Histone H2A type 1-B/E HIST1H2AB Secreted Nucleus. Detection, Prediction
H2A1C Histone H2A type 1-C HIST1H2AC Secreted Nucleus. Literature, Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
H2A1D Histone H2A type 1-D HIST1H2AD Secreted Nucleus. Detection, Prediction
HG2A HLA class II histocompatibility antigen gamma chain
CD74 LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type II membrane protein (Potential).
UniProt, Literature
HGF Hepatocyte growth factor HGF LungCancers, BenignNodules, Symptoms
Literature, Prediction
HMGA1 High mobility group protein HMG-I/HMG-Y
HMGA1 LungCancers, BenignNodules, Symptoms
Nucleus. Literature
HPRT Hypoxanthine-guanine phosphoribosyltransferase
HPRT1 EPI Cytoplasm. Detection, Prediction
HPSE Heparanase HPSE LungCancers, BenignNodules, Symptoms
Lysosome membrane; Peripheral membrane protein. Secreted. Note=Secreted, internalised and transferred to late endosomes/lysosomes as a proheparanase. In lysosomes, it is processed into the active form, the heparanase. The uptake or internalisation of proheparanase is mediated by HSPGs. Heparin appears to be a competitor and retain proheparanase in the extracellular medium.
UniProt, Prediction
HPT Haptoglobin HP LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
HS90A Heat shock protein HSP 90-alpha
HSP90AA1 Secreted, EPI LungCancers, Symptoms
Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection
HS90B Heat shock protein HSP 90-beta HSP90AB1 Secreted, EPI LungCancers Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Literature, Detection
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
HSPB1 Heat shock protein beta-1 HSPB1 Secreted, EPI LungCancers, BenignNodules
Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, spindle. Note=Cytoplasmic in interphase cells. Colocalizes with mitotic spindles in mitotic cells. Translocates to the nucleus during heat shock.
Literature, Detection, Prediction
HTRA1 Serine protease HTRA1 HTRA1 LungCancers Secreted. UniProt, Prediction
HXK1 Hexokinase-1 HK1 ENDO Symptoms Mitochondrion outer membrane. Note=Its hydrophobic N-terminal sequence may be involved in membrane binding.
Literature, Detection
HYAL2 Hyaluronidase-2 HYAL2 LungCancers Cell membrane; Lipid-anchor, GPI-anchor. Prediction HYOU1 Hypoxia up-regulated protein 1 HYOU1 EPI, ENDO Symptoms Endoplasmic reticulum lumen. Detection IBP2 Insulin-like growth factor-
binding protein 2 IGFBP2 LungCancers Secreted. UniProt,
Literature, Detection, Prediction
IBP3 Insulin-like growth factor-binding protein 3
IGFBP3 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
ICAM1 Intercellular adhesion molecule 1
ICAM1 LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
ICAM3 Intercellular adhesion molecule 3
ICAM3 EPI, ENDO LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Detection
IDHP Isocitrate dehydrogenase [NADP], mitochondrial
IDH2 Secreted, ENDO
Mitochondrion. Prediction
IF4A1 Eukaryotic initiation factor 4A-I
EIF4A1 Secreted, EPI, ENDO
Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
IGF1 Insulin-like growth factor I IGF1 LungCancers, BenignNodules, Symptoms
Secreted.|Secreted. UniProt, Literature, Detection, Prediction
IKIP Inhibitor of nuclear factor kappa-B kinase-interacting protein
IKIP ENDO Symptoms Endoplasmic reticulum membrane; Single-pass membrane protein. Note=Isoform 4 deletion of the hydrophobic, or transmembrane region between AA 45-63 results in uniform distribution troughout the cell, suggesting that this region is responsible for endoplasmic reticulum localization.
UniProt, Prediction
IL18 Interleukin-18 IL18 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Prediction
IL19 Interleukin-19 IL19 LungCancers Secreted. UniProt, Detection, Prediction
IL22 Interleukin-22 IL22 LungCancers, BenignNodules
Secreted. UniProt, Prediction
IL32 Interleukin-32 IL32 LungCancers, BenignNodules
Secreted. UniProt, Prediction
IL7 Interleukin-7 IL7 LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
IL8 Interleukin-8 IL8 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature
ILEU Leukocyte elastase inhibitor SERPINB1 Secreted, EPI Cytoplasm (By similarity). Detection, Prediction
ILK Integrin-linked protein kinase ILK Secreted LungCancers, BenignNodules, Symptoms
Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side.
Literature, Detection
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
INHBA Inhibin beta A chain INHBA LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
ISLR Immunoglobulin superfamily containing leucine-rich repeat protein
ISLR LungCancers Secreted (Potential). UniProt, Detection, Prediction
ITA5 Integrin alpha-5 ITGA5 EPI LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
ITAM Integrin alpha-M ITGAM EPI, ENDO LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature
K0090 Uncharacterized protein KIAA0090
KIAA0090 EPI Symptoms Membrane; Single-pass type I membrane protein (Potential).
UniProt, Prediction
K1C18 Keratin, type I cytoskeletal 18 KRT18 Secreted LungCancers, BenignNodules
Cytoplasm, perinuclear region. Literature, Detection, Prediction
K1C19 Keratin, type I cytoskeletal 19 KRT19 LungCancers, BenignNodules
Literature, Detection, Prediction
K2C8 Keratin, type II cytoskeletal 8 KRT8 EPI LungCancers Cytoplasm. Literature, Detection
KIT Mast/stem cell growth factor receptor
KIT LungCancers Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
KITH Thymidine kinase, cytosolic TK1 LungCancers Cytoplasm. Literature, Prediction
KLK11 Kallikrein-11 KLK11 LungCancers Secreted. UniProt, Literature, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
KLK13 Kallikrein-13 KLK13 LungCancers Secreted (Probable). UniProt, Literature, Detection, Prediction
KLK14 Kallikrein-14 KLK14 LungCancers, Symptoms
Secreted, extracellular space. UniProt, Literature, Prediction
KLK6 Kallikrein-6 KLK6 LungCancers, BenignNodules, Symptoms
Secreted. Nucleus, nucleolus. Cytoplasm. Mitochondrion. Microsome. Note=In brain, detected in the nucleus of glial cells and in the nucleus and cytoplasm of neurons. Detected in the mitochondrial and microsomal fractions of HEK-293 cells and released into the cytoplasm following cell stress.
UniProt, Literature, Detection, Prediction
KNG1 Kininogen-1 KNG1 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space. UniProt, Detection, Prediction
KPYM Pyruvate kinase isozymes M1/M2
PKM2 Secreted, EPI LungCancers, Symptoms
Cytoplasm. Nucleus. Note=Translocates to the nucleus in response to different apoptotic stimuli. Nuclear translocation is sufficient to induce cell death that is caspase independent, isoform-specific and independent of its enzymatic actvity.
Literature, Detection
KRT35 Keratin, type I cuticular Ha5 KRT35 ENDO Detection, Prediction
LAMB2 Laminin subunit beta-2 LAMB2 ENDO LungCancers, Symptoms
Secreted, extracellular space, extracellular matrix, basement membrane. Note=S-laminin is concentrated in the synaptic cleft of the neuromuscular junction.
UniProt, Detection, Prediction
LDHA L-lactate dehydrogenase A chain
LDHA Secreted, EPI, ENDO
LungCancers Cytoplasm. Literature, Detection, Prediction
Submitted Manuscript: Confidential
47
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
LDHB L-lactate dehydrogenase B chain
LDHB EPI LungCancers Cytoplasm. Detection, Prediction
LEG1 Galectin-1 LGALS1 Secreted LungCancers Secreted, extracellular space, extracellular matrix.
UniProt, Detection
LEG3 Galectin-3 LGALS3 LungCancers, BenignNodules
Nucleus. Note=Cytoplasmic in adenomas and carcinomas. May be secreted by a non-classical secretory pathway and associate with the cell surface.
Literature, Detection, Prediction
LEG9 Galectin-9 LGALS9 ENDO Symptoms Cytoplasm (By similarity). Secreted (By similarity). Note=May also be secreted by a non-classical secretory pathway (By similarity).
UniProt
LG3BP Galectin-3-binding protein LGALS3BP Secreted LungCancers, BenignNodules, Symptoms
Secreted. Secreted, extracellular space, extracellular matrix.
UniProt, Literature, Detection, Prediction
LPLC3 Long palate, lung and nasal epithelium carcinoma-associated protein 3
C20orf185 LungCancers Secreted (By similarity). Cytoplasm. Note=According to PubMed:12837268 it is cytoplasmic.
UniProt, Prediction
LPLC4 Long palate, lung and nasal epithelium carcinoma-associated protein 4
C20orf186 LungCancers Secreted (By similarity). Cytoplasm. UniProt, Prediction
LPPRC Leucine-rich PPR motif-containing protein, mitochondrial
LRPPRC Secreted, ENDO
LungCancers, Symptoms
Mitochondrion. Nucleus, nucleoplasm. Nucleus inner membrane. Nucleus outer membrane. Note=Seems to be predominantly mitochondrial.
Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
LRP1 Prolow-density lipoprotein receptor-related protein 1
LRP1 EPI LungCancers, Symptoms
Low-density lipoprotein receptor-related protein 1 85 kDa subunit: Cell membrane; Single-pass type I membrane protein. Membrane, coated pit.|Low-density lipoprotein receptor-related protein 1 515 kDa subunit: Cell membrane; Peripheral membrane protein; Extracellular side. Membrane, coated pit.|Low-density lipoprotein receptor-related protein 1 intracellular domain: Cytoplasm. Nucleus. Note=After cleavage, the intracellular domain (LRPICD) is detected both in the cytoplasm and in the nucleus.
UniProt, Detection
LUM Lumican LUM Secreted, EPI LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Detection, Prediction
LY6K Lymphocyte antigen 6K LY6K LungCancers, Symptoms
Secreted. Cytoplasm. Cell membrane; Lipid- anchor, GPI-anchor (Potential).
UniProt, Prediction
LYAM2 E-selectin SELE LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
LYAM3 P-selectin SELP LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
LYOX Protein-lysine 6-oxidase LOX LungCancers, BenignNodules
Secreted, extracellular space. UniProt, Detection, Prediction
LYPD3 Ly6/PLAUR domain-containing protein 3
LYPD3 LungCancers Cell membrane; Lipid-anchor, GPI-anchor. Detection, Prediction
MAGA4 Melanoma-associated antigen 4 MAGEA4 LungCancers Literature, Prediction
Submitted Manuscript: Confidential
49
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
MASP1 Mannan-binding lectin serine protease 1
MASP1 LungCancers, Symptoms
Secreted. UniProt, Detection, Prediction
MDHC Malate dehydrogenase, cytoplasmic
MDH1 Secreted Cytoplasm. Literature, Detection, Prediction
MDHM Malate dehydrogenase, mitochondrial
MDH2 ENDO LungCancers Mitochondrion matrix. Detection, Prediction
MIF Macrophage migration inhibitory factor
MIF Secreted LungCancers, BenignNodules, Symptoms
Secreted. Cytoplasm. Note=Does not have a cleavable signal sequence and is secreted via a specialized, non- classical pathway. Secreted by macrophages upon stimulation by bacterial lipopolysaccharide (LPS), or by M.tuberculosis antigens.
UniProt, Literature, Prediction
MLH1 DNA mismatch repair protein Mlh1
MLH1 ENDO LungCancers, BenignNodules, Symptoms
Nucleus. Literature
MMP1 Interstitial collagenase MMP1 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Prediction
MMP11 Stromelysin-3 MMP11 LungCancers, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Prediction
MMP12 Macrophage metalloelastase MMP12 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Prediction
MMP14 Matrix metalloproteinase-14 MMP14 ENDO LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein (Potential). Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
UniProt, Literature, Detection
Submitted Manuscript: Confidential
50
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
MMP2 72 kDa type IV collagenase MMP2 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Detection, Prediction
MMP26 Matrix metalloproteinase-26 MMP26 LungCancers Secreted, extracellular space, extracellular matrix.
UniProt, Prediction
MMP7 Matrilysin MMP7 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Prediction
MMP9 Matrix metalloproteinase-9 MMP9 LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix (Probable).
UniProt, Literature, Detection, Prediction
MOGS Mannosyl-oligosaccharide glucosidase
MOGS ENDO Endoplasmic reticulum membrane; Single-pass type II membrane protein.
UniProt, Prediction
MPRI Cation-independent mannose-6-phosphate receptor
IGF2R EPI, ENDO LungCancers, Symptoms
Lysosome membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
MRP3 Canalicular multispecific organic anion transporter 2
ABCC3 EPI LungCancers Membrane; Multi-pass membrane protein. Literature, Detection
Submitted Manuscript: Confidential
51
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
MUC1 Mucin-1 MUC1 EPI LungCancers, BenignNodules, Symptoms
Apical cell membrane; Single-pass type I membrane protein. Note=Exclusively located in the apical domain of the plasma membrane of highly polarized epithelial cells. After endocytosis, internalized and recycled to the cell membrane. Located to microvilli and to the tips of long filopodial protusions.|Isoform 5: Secreted.|Isoform 7: Secreted.|Isoform 9: Secreted.|Mucin-1 subunit beta: Cell membrane. Cytoplasm. Nucleus. Note=On EGF and PDGFRB stimulation, transported to the nucleus through interaction with CTNNB1, a process which is stimulated by phosphorylation. On HRG stimulation, colocalizes with JUP/gamma-catenin at the nucleus.
UniProt, Literature, Prediction
MUC16 Mucin-16 MUC16 LungCancers Cell membrane; Single-pass type I membrane protein. Secreted, extracellular space. Note=May be liberated into the extracellular space following the phosphorylation of the intracellular C-terminus which induces the proteolytic cleavage and liberation of the extracellular domain.
UniProt, Detection
Submitted Manuscript: Confidential
52
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
MUC4 Mucin-4 MUC4 LungCancers, BenignNodules
Membrane; Single-pass membrane protein (Potential). Secreted. Note=Isoforms lacking the Cys-rich region, EGF-like domains and transmembrane region are secreted. Secretion occurs by splicing or proteolytic processing.|Mucin-4 beta chain: Cell membrane; Single- pass membrane protein.|Mucin-4 alpha chain: Secreted.|Isoform 3: Cell membrane; Single-pass membrane protein.|Isoform 15: Secreted.
UniProt
MUC5B Mucin-5B MUC5B LungCancers, BenignNodules
Secreted. UniProt, Detection, Prediction
MUCL1 Mucin-like protein 1 MUCL1 LungCancers Secreted (Probable). Membrane (Probable). UniProt, Prediction
NAMPT Nicotinamide phosphoribosyltransferase
NAMPT EPI LungCancers, BenignNodules, Symptoms
Cytoplasm (By similarity). Literature, Detection
NAPSA Napsin-A NAPSA Secreted LungCancers Prediction NCF4 Neutrophil cytosol factor 4 NCF4 ENDO Cytoplasm. Prediction NDKA Nucleoside diphosphate kinase
A NME1 Secreted LungCancers,
BenignNodules, Symptoms
Cytoplasm. Nucleus. Note=Cell-cycle dependent nuclear localization which can be induced by interaction with Epstein-barr viral proteins or by degradation of the SET complex by GzmA.
Literature, Detection
NDKB Nucleoside diphosphate kinase B
NME2 Secreted, EPI BenignNodules Cytoplasm. Nucleus. Note=Isoform 2 is mainly cytoplasmic and isoform 1 and isoform 2 are excluded from the nucleolus.
Literature, Detection
NDUS1 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
NDUFS1 Secreted, ENDO
Symptoms Mitochondrion inner membrane. Prediction
NEBL Nebulette NEBL ENDO Prediction
Submitted Manuscript: Confidential
53
Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
NEK4 Serine/threonine-protein kinase Nek4
NEK4 ENDO LungCancers Nucleus (Probable). Prediction
NET1 Netrin-1 NTN1 LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Literature, Prediction
NEU2 Vasopressin-neurophysin 2-copeptin
AVP LungCancers, Symptoms
Secreted. UniProt, Prediction
NGAL Neutrophil gelatinase-associated lipocalin
LCN2 EPI LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Detection, Prediction
NGLY1 Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
NGLY1 ENDO Cytoplasm. Detection, Prediction
NHRF1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1
SLC9A3R1 EPI BenignNodules Endomembrane system; Peripheral membrane protein. Cell projection, filopodium. Cell projection, ruffle. Cell projection, microvillus. Note=Colocalizes with actin in microvilli-rich apical regions of the syncytiotrophoblast. Found in microvilli, ruffling membrane and filopodia of HeLa cells. Present in lipid rafts of T-cells.
Detection
NIBAN Protein Niban FAM129A EPI Cytoplasm. Literature, Detection
NMU Neuromedin-U NMU LungCancers Secreted. UniProt, Prediction
NRP1 Neuropilin-1 NRP1 LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type I membrane protein.|Isoform 2: Secreted.
UniProt, Literature, Detection, Prediction
ODAM Odontogenic ameloblast-associated protein
ODAM LungCancers Secreted (By similarity). UniProt, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
OSTP Osteopontin SPP1 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
OVOS2 Ovostatin homolog 2 OVOS2 ENDO Secreted (By similarity). UniProt, Prediction
P5CS Delta-1-pyrroline-5-carboxylate synthase
ALDH18A1 ENDO Mitochondrion inner membrane. Prediction
PA2GX Group 10 secretory phospholipase A2
PLA2G10 Symptoms Secreted. UniProt
PAPP1 Pappalysin-1 PAPPA LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Prediction
PBIP1 Pre-B-cell leukemia transcription factor-interacting protein 1
PBXIP1 EPI Cytoplasm, cytoskeleton. Nucleus. Note=Shuttles between the nucleus and the cytosol. Mainly localized in the cytoplasm, associated with microtubules. Detected in small amounts in the nucleus.
Prediction
PCBP1 Poly(rC)-binding protein 1 PCBP1 EPI, ENDO Nucleus. Cytoplasm. Note=Loosely bound in the nucleus. May shuttle between the nucleus and the cytoplasm.
Detection, Prediction
PCBP2 Poly(rC)-binding protein 2 PCBP2 EPI Nucleus. Cytoplasm. Note=Loosely bound in the nucleus. May shuttle between the nucleus and the cytoplasm.
Detection, Prediction
PCD15 Protocadherin-15 PCDH15 ENDO Cell membrane; Single-pass type I membrane protein (By similarity).|Isoform 3: Secreted.
UniProt, Detection
PCNA Proliferating cell nuclear antigen
PCNA EPI LungCancers, BenignNodules, Symptoms
Nucleus. Literature, Prediction
PCYOX Prenylcysteine oxidase 1 PCYOX1 Secreted LungCancers, Symptoms
Lysosome. Detection, Prediction
Submitted Manuscript: Confidential
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
PDGFA Platelet-derived growth factor subunit A
PDGFA LungCancers Secreted. UniProt, Literature, Prediction
PDGFB Platelet-derived growth factor subunit B
PDGFB LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
PDGFD Platelet-derived growth factor D
PDGFD LungCancers Secreted. UniProt, Prediction
PDIA3 Protein disulfide-isomerase A3 PDIA3 ENDO LungCancers Endoplasmic reticulum lumen (By similarity). Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
PDIA4 Protein disulfide-isomerase A4 PDIA4 Secreted, EPI, ENDO
Endoplasmic reticulum lumen. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
PDIA6 Protein disulfide-isomerase A6 PDIA6 Secreted, EPI, ENDO
Endoplasmic reticulum lumen (By similarity). Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
PECA1 Platelet endothelial cell adhesion molecule
PECAM1 LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
PEDF Pigment epithelium-derived factor
SERPINF1 LungCancers, Symptoms
Secreted. Melanosome. Note=Enriched in stage I melanosomes.
UniProt, Literature, Detection, Prediction
PERM Myeloperoxidase MPO Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Lysosome. Literature, Detection, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
PERP1 Plasma cell-induced resident endoplasmic reticulum protein
PACAP EPI, ENDO Secreted (Potential). Cytoplasm. Note=In (PubMed:11350957) diffuse granular localization in the cytoplasm surrounding the nucleus.
UniProt, Detection, Prediction
PGAM1 Phosphoglycerate mutase 1 PGAM1 Secreted, EPI LungCancers, Symptoms
Detection
PLAC1 Placenta-specific protein 1 PLAC1 LungCancers Secreted (Probable). UniProt, Prediction
PLACL Placenta-specific 1-like protein PLAC1L LungCancers Secreted (Potential). UniProt, Prediction
PLIN2 Perilipin-2 ADFP ENDO LungCancers Membrane; Peripheral membrane protein. Prediction PLIN3 Perilipin-3 M6PRBP1 EPI Cytoplasm. Endosome membrane;
Peripheral membrane protein; Cytoplasmic side (Potential). Lipid droplet (Potential). Note=Membrane associated on endosomes. Detected in the envelope and the core of lipid bodies and in lipid sails.
Detection, Prediction
PLOD1 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
PLOD1 EPI, ENDO Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.
Prediction
PLOD2 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
PLOD2 ENDO BenignNodules, Symptoms
Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.
Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
PLSL Plastin-2 LCP1 Secreted, EPI LungCancers Cytoplasm, cytoskeleton. Cell junction. Cell projection. Cell projection, ruffle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=Relocalizes to the immunological synapse between peripheral blood T lymphocytes and antibody-presenting cells in response to costimulation through TCR/CD3 and CD2 or CD28. Associated with the actin cytoskeleton at membrane ruffles (By similarity). Relocalizes to actin-rich cell projections upon serine phosphorylation.
Detection, Prediction
PLUNC Protein Plunc PLUNC LungCancers, BenignNodules
Secreted (By similarity). Note=Found in the nasal mucus (By similarity). Apical side of airway epithelial cells. Detected in nasal mucus (By similarity).
UniProt, Prediction
PLXB3 Plexin-B3 PLXNB3 ENDO Membrane; Single-pass type I membrane protein.
UniProt, Detection, Prediction
PLXC1 Plexin-C1 PLXNC1 EPI Membrane; Single-pass type I membrane protein (Potential).
UniProt, Detection
POSTN Periostin POSTN Secreted, ENDO
LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix.
UniProt, Literature, Detection, Prediction
PPAL Lysosomal acid phosphatase ACP2 EPI Symptoms Lysosome membrane; Single-pass membrane protein; Lumenal side. Lysosome lumen. Note=The soluble form arises by proteolytic processing of the membrane-bound form.
UniProt, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
PPBT Alkaline phosphatase, tissue-nonspecific isozyme
ALPL EPI LungCancers, BenignNodules, Symptoms
Cell membrane; Lipid-anchor, GPI-anchor. Literature, Detection, Prediction
PPIB Peptidyl-prolyl cis-trans isomerase B
PPIB Secreted, EPI, ENDO
Endoplasmic reticulum lumen. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
PRDX1 Peroxiredoxin-1 PRDX1 EPI LungCancers Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
PRDX4 Peroxiredoxin-4 PRDX4 Secreted, EPI, ENDO
Cytoplasm. Literature, Detection, Prediction
PROF1 Profilin-1 PFN1 Secreted, EPI LungCancers Cytoplasm, cytoskeleton. Detection PRP31 U4/U6 small nuclear
ribonucleoprotein Prp31 PRPF31 ENDO Nucleus speckle. Nucleus, Cajal body.
Note=Predominantly found in speckles and in Cajal bodies.
Prediction
PRS6A 26S protease regulatory subunit 6A
PSMC3 EPI BenignNodules Cytoplasm (Potential). Nucleus (Potential). Detection
PSCA Prostate stem cell antigen PSCA LungCancers Cell membrane; Lipid-anchor, GPI-anchor. Literature, Prediction
PTGIS Prostacyclin synthase PTGIS EPI LungCancers, BenignNodules
Endoplasmic reticulum membrane; Single-pass membrane protein.
UniProt, Detection, Prediction
PTPA Serine/threonine-protein phosphatase 2A activator
PPP2R4 ENDO Symptoms Detection, Prediction
PTPRC Receptor-type tyrosine-protein phosphatase C
PTPRC Secreted, EPI, ENDO
LungCancers Membrane; Single-pass type I membrane protein.
UniProt, Detection, Prediction
PTPRJ Receptor-type tyrosine-protein phosphatase eta
PTPRJ EPI LungCancers, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Detection, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
PVR Poliovirus receptor PVR Symptoms Isoform Alpha: Cell membrane; Single-pass type I membrane protein.|Isoform Delta: Cell membrane; Single-pass type I membrane protein.|Isoform Beta: Secreted.|Isoform Gamma: Secreted.
UniProt, Detection, Prediction
RAB32 Ras-related protein Rab-32 RAB32 EPI Mitochondrion. Prediction RAGE Advanced glycosylation end
product-specific receptor AGER Secreted LungCancers,
BenignNodules Isoform 1: Cell membrane; Single-pass type I membrane protein.|Isoform 2: Secreted.
UniProt, Literature
RAN GTP-binding nuclear protein Ran
RAN Secreted, EPI LungCancers, BenignNodules
Nucleus. Cytoplasm. Melanosome. Note=Becomes dispersed throughout the cytoplasm during mitosis. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
RAP2B Ras-related protein Rap-2b RAP2B EPI Cell membrane; Lipid-anchor; Cytoplasmic side (Potential).
Prediction
RAP2C Ras-related protein Rap-2c RAP2C EPI Cell membrane; Lipid-anchor; Cytoplasmic side (Potential).
Prediction
RCN3 Reticulocalbin-3 RCN3 EPI Symptoms Endoplasmic reticulum lumen (Potential). Prediction RL24 60S ribosomal protein L24 RPL24 EPI Prediction S10A1 Protein S100-A1 S100A1 Symptoms Cytoplasm. Literature,
Prediction S10A6 Protein S100-A6 S100A6 Secreted LungCancers Nucleus envelope. Cytoplasm. Literature,
Detection, Prediction
S10A7 Protein S100-A7 S100A7 LungCancers Cytoplasm. Secreted. Note=Secreted by a non- classical secretory pathway.
UniProt, Literature, Detection, Prediction
SAA Serum amyloid A protein SAA1 Symptoms Secreted. UniProt, Literature, Detection, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
SCF Kit ligand KITLG LungCancers, Symptoms
Isoform 1: Cell membrane; Single-pass type I membrane protein (By similarity). Secreted (By similarity). Note=Also exists as a secreted soluble form (isoform 1 only) (By similarity).|Isoform 2: Cell membrane; Single-pass type I membrane protein (By similarity). Cytoplasm, cytoskeleton (By similarity).
UniProt, Literature
SDC1 Syndecan-1 SDC1 LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature, Detection
SEM3G Semaphorin-3G SEMA3G LungCancers Secreted (By similarity). UniProt, Prediction
SEPR Seprase FAP ENDO Symptoms Cell membrane; Single-pass type II membrane protein. Cell projection, lamellipodium membrane; Single-pass type II membrane protein. Cell projection, invadopodium membrane; Single-pass type II membrane protein. Note=Found in cell surface lamellipodia, invadopodia and on shed vesicles.
UniProt, Literature, Detection
SERPH Serpin H1 SERPINH1 Secreted, EPI, ENDO
LungCancers, BenignNodules
Endoplasmic reticulum lumen. Detection, Prediction
SFPA2 Pulmonary surfactant-associated protein A2
SFTPA2 Secreted LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix. Secreted, extracellular space, surface film.
UniProt, Prediction
SFTA1 Pulmonary surfactant-associated protein A1
SFTPA1 Secreted LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix. Secreted, extracellular space, surface film.
UniProt, Prediction
SG3A2 Secretoglobin family 3A member 2
SCGB3A2 LungCancers, BenignNodules
Secreted. UniProt, Prediction
SGPL1 Sphingosine-1-phosphate lyase 1
SGPL1 ENDO Endoplasmic reticulum membrane; Single-pass type III membrane protein.
UniProt, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
SIAL Bone sialoprotein 2 IBSP LungCancers Secreted. UniProt, Literature, Prediction
SLPI Antileukoproteinase SLPI LungCancers, BenignNodules
Secreted. UniProt, Literature, Detection, Prediction
SMD3 Small nuclear ribonucleoprotein Sm D3
SNRPD3 Secreted BenignNodules Nucleus. Prediction
SMS Somatostatin SST LungCancers Secreted. UniProt, Literature, Prediction
SODM Superoxide dismutase [Mn], mitochondrial
SOD2 Secreted LungCancers, BenignNodules, Symptoms
Mitochondrion matrix. Literature, Detection, Prediction
SORL Sortilin-related receptor SORL1 EPI LungCancers, Symptoms
Membrane; Single-pass type I membrane protein (Potential).
UniProt, Detection
SPB3 Serpin B3 SERPINB3 LungCancers, BenignNodules
Cytoplasm. Note=Seems to also be secreted in plasma by cancerous cells but at a low level.
Literature, Detection
SPB5 Serpin B5 SERPINB5 LungCancers Secreted, extracellular space. UniProt, Detection
SPON2 Spondin-2 SPON2 LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix (By similarity).
UniProt, Prediction
SPRC SPARC SPARC LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix, basement membrane. Note=In or around the basement membrane.
UniProt, Literature, Detection, Prediction
SRC Proto-oncogene tyrosine-protein kinase Src
SRC ENDO LungCancers, BenignNodules, Symptoms
Literature
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
SSRD Translocon-associated protein subunit delta
SSR4 Secreted, ENDO
Endoplasmic reticulum membrane; Single-pass type I membrane protein.
UniProt, Prediction
STAT1 Signal transducer and activator of transcription 1-alpha/beta
STAT1 EPI LungCancers, BenignNodules
Cytoplasm. Nucleus. Note=Translocated into the nucleus in response to IFN-gamma-induced tyrosine phosphorylation and dimerization.
Detection
STAT3 Signal transducer and activator of transcription 3
STAT3 ENDO LungCancers, BenignNodules, Symptoms
Cytoplasm. Nucleus. Note=Shuttles between the nucleus and the cytoplasm. Constitutive nuclear presence is independent of tyrosine phosphorylation.
Prediction
STC1 Stanniocalcin-1 STC1 LungCancers, Symptoms
Secreted. UniProt, Prediction
STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
STT3A EPI Symptoms Endoplasmic reticulum membrane; Multi-pass membrane protein.
Literature
TAGL Transgelin TAGLN EPI LungCancers Cytoplasm (Probable). Literature, Prediction
TARA TRIO and F-actin-binding protein
TRIOBP ENDO Nucleus. Cytoplasm, cytoskeleton. Note=Localized to F-actin in a periodic pattern.
Detection, Prediction
TBA1B Tubulin alpha-1B chain TUBA1B EPI LungCancers Detection TBB2A Tubulin beta-2A chain TUBB2A EPI LungCancers,
BenignNodules Detection,
Prediction TBB3 Tubulin beta-3 chain TUBB3 EPI LungCancers,
BenignNodules Detection
TBB5 Tubulin beta chain TUBB EPI LungCancers, BenignNodules
Detection
TCPA T-complex protein 1 subunit alpha
TCP1 EPI Cytoplasm. Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
TCPD T-complex protein 1 subunit delta
CCT4 EPI Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
Detection, Prediction
TCPQ T-complex protein 1 subunit theta
CCT8 Secreted, EPI Cytoplasm. Prediction
TCPZ T-complex protein 1 subunit zeta
CCT6A Secreted, EPI Cytoplasm. Detection
TDRD3 Tudor domain-containing protein 3
TDRD3 ENDO Cytoplasm. Nucleus. Note=Predominantly cytoplasmic. Associated with actively translating polyribosomes and with mRNA stress granules.
Prediction
TENA Tenascin TNC ENDO LungCancers, BenignNodules, Symptoms
Secreted, extracellular space, extracellular matrix.
UniProt, Literature, Detection
TENX Tenascin-X TNXB ENDO LungCancers, Symptoms
Secreted, extracellular space, extracellular matrix.
UniProt, Detection, Prediction
TERA Transitional endoplasmic reticulum ATPase
VCP EPI LungCancers, BenignNodules
Cytoplasm, cytosol. Nucleus. Note=Present in the neuronal hyaline inclusion bodies specifically found in motor neurons from amyotrophic lateral sclerosis patients. Present in the Lewy bodies specifically found in neurons from Parkinson disease patients.
Detection
TETN Tetranectin CLEC3B LungCancers Secreted. UniProt, Literature, Detection, Prediction
TF Tissue factor F3 LungCancers, BenignNodules, Symptoms
Membrane; Single-pass type I membrane protein.
UniProt, Literature
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
TFR1 Transferrin receptor protein 1 TFRC Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Cell membrane; Single-pass type II membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.|Transferrin receptor protein 1, serum form: Secreted.
UniProt, Literature, Detection
TGFA Protransforming growth factor alpha
TGFA LungCancers, BenignNodules
Transforming growth factor alpha: Secreted, extracellular space.|Protransforming growth factor alpha: Cell membrane; Single-pass type I membrane protein.
UniProt, Literature
THAS Thromboxane-A synthase TBXAS1 EPI, ENDO LungCancers, BenignNodules, Symptoms
Membrane; Multi-pass membrane protein. Prediction
THY1 Thy-1 membrane glycoprotein THY1 EPI Symptoms Cell membrane; Lipid-anchor, GPI-anchor (By similarity).
Detection, Prediction
TIMP1 Metalloproteinase inhibitor 1 TIMP1 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
TIMP3 Metalloproteinase inhibitor 3 TIMP3 LungCancers, BenignNodules
Secreted, extracellular space, extracellular matrix.
UniProt, Literature, Prediction
TLL1 Tolloid-like protein 1 TLL1 ENDO Secreted (Probable). UniProt, Prediction
TNF12 Tumor necrosis factor ligand superfamily member 12
TNFSF12 LungCancers, BenignNodules
Cell membrane; Single-pass type II membrane protein.|Tumor necrosis factor ligand superfamily member 12, secreted form: Secreted.
UniProt
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
TNR6 Tumor necrosis factor receptor superfamily member 6
FAS LungCancers, BenignNodules, Symptoms
Isoform 1: Cell membrane; Single-pass type I membrane protein.|Isoform 2: Secreted.|Isoform 3: Secreted.|Isoform 4: Secreted.|Isoform 5: Secreted.|Isoform 6: Secreted.
UniProt, Literature, Prediction
TPIS Triosephosphate isomerase TPI1 Secreted, EPI Symptoms Literature, Detection, Prediction
TRFL Lactotransferrin LTF Secreted, EPI, ENDO
LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
TSP1 Thrombospondin-1 THBS1 LungCancers, BenignNodules, Symptoms
Literature, Detection, Prediction
TTHY Transthyretin TTR LungCancers, BenignNodules
Secreted. Cytoplasm. UniProt, Literature, Detection, Prediction
TYPH Thymidine phosphorylase TYMP EPI LungCancers, BenignNodules, Symptoms
Literature, Detection, Prediction
UGGG1 UDP-glucose:glycoprotein glucosyltransferase 1
UGGT1 Secreted, ENDO
Endoplasmic reticulum lumen. Endoplasmic reticulum-Golgi intermediate compartment.
Detection, Prediction
UGGG2 UDP-glucose:glycoprotein glucosyltransferase 2
UGGT2 ENDO Endoplasmic reticulum lumen. Endoplasmic reticulum-Golgi intermediate compartment.
Prediction
UGPA UTP--glucose-1-phosphate uridylyltransferase
UGP2 EPI Symptoms Cytoplasm. Detection
UPAR Urokinase plasminogen activator surface receptor
PLAUR LungCancers, BenignNodules, Symptoms
Isoform 1: Cell membrane; Lipid-anchor, GPI- anchor.|Isoform 2: Secreted (Probable).
UniProt, Literature, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
UTER Uteroglobin SCGB1A1 LungCancers, BenignNodules, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
VA0D1 V-type proton ATPase subunit d 1
ATP6V0D1 EPI Prediction
VAV3 Guanine nucleotide exchange factor VAV3
VAV3 ENDO Prediction
VEGFA Vascular endothelial growth factor A
VEGFA LungCancers, BenignNodules, Symptoms
Secreted. Note=VEGF121 is acidic and freely secreted. VEGF165 is more basic, has heparin-binding properties and, although a signicant proportion remains cell-associated, most is freely secreted. VEGF189 is very basic, it is cell-associated after secretion and is bound avidly by heparin and the extracellular matrix, although it may be released as a soluble form by heparin, heparinase or plasmin.
UniProt, Literature, Prediction
VEGFC Vascular endothelial growth factor C
VEGFC LungCancers, BenignNodules
Secreted. UniProt, Literature, Prediction
VEGFD Vascular endothelial growth factor D
FIGF LungCancers Secreted. UniProt, Literature, Prediction
VGFR1 Vascular endothelial growth factor receptor 1
FLT1 LungCancers, BenignNodules, Symptoms
Isoform Flt1: Cell membrane; Single-pass type I membrane protein.|Isoform sFlt1: Secreted.
UniProt, Literature, Detection, Prediction
VTNC Vitronectin VTN ENDO Symptoms Secreted, extracellular space. UniProt, Literature, Detection, Prediction
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Table S3. Information of 388 protein candidates. Protein (HUMAN)
Protein name Gene symbol Source of tissue biomarkers
Biomarkers in literature
Subcellular location (UniProt) Evidence for presence in blood
VWC2 Brorin VWC2 LungCancers Secreted, extracellular space, extracellular matrix, basement membrane (By similarity).
UniProt, Prediction
WNT3A Protein Wnt-3a WNT3A LungCancers, Symptoms
Secreted, extracellular space, extracellular matrix.
UniProt, Prediction
WT1 Wilms tumor protein WT1 LungCancers, BenignNodules, Symptoms
Nucleus. Cytoplasm (By similarity). Note=Shuttles between nucleus and cytoplasm (By similarity).|Isoform 1: Nucleus speckle.|Isoform 4: Nucleus, nucleoplasm.
Literature, Prediction
ZA2G Zinc-alpha-2-glycoprotein AZGP1 LungCancers, Symptoms
Secreted. UniProt, Literature, Detection, Prediction
ZG16B Zymogen granule protein 16 homolog B
ZG16B LungCancers Secreted (Potential). UniProt, Prediction
Note: • Source of tissue biomarkers
Datasets from which the protein was identified as a tissue biomarker: Secreted (secretory vesicles of 33 lung cancer patients, including 13 adenocarcinoma, 5 large cell carcinoma and 15 squamous cell carcinoma), EPI (membrane vesicles of epithelial cells of 30 lung cancer patients, including 19 adenocarcinoma, 5 large cell carcinoma, and 6 squamous cell carcinoma), and ENDO (membrane vesicles of endothelial cells of 38 lung cancer patients, including 13 adenocarcinoma, 7 large cell carcinoma, and 18 squamous cell carcinoma): See Table S1.
• Biomarkers in literature Terminologies with which the protein or the corresponding gene was associated in the literature: LungCancers (subtypes of lung cancers), BenignNodules (diseases causing benign lung nodules), and Symptoms (symptoms of benign or cancerous lung nodules): See Table S2.
• Evidence for presence in blood
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Evidence for presence in blood based on four sources: UniProt (annotated as a secreted protein or a single-pass transmembrane protein), Literature (57), Detection (previously detected in blood samples by mass spectrometry (54-56)), or Prediction (predicted as a secreted protein by TMHMM (58), SignalP (59), and/or SecretomeP (60)).
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Table S4. Summary of protein MRM assay development and detection in blood.
Characteristic Selected for assay development
Developed MRM assays
Success rate (%)
Detected in blood
Detection rate (%)
Source of candidates
Tissue biomarkers & biomarkers in literature
148 146 98.6 91 62.3
Tissue biomarkers only 69 69 100.0 23 33.3 Biomarkers in literature only 171 156 91.2 76 48.7 All tissue biomarkers 217 215 99.1 114 53.0 All biomarkers in literature 319 302 94.7 167 55.3 Evidence for presence in blood (see Table S3) UniProt, Literature, Detection & Prediction
42 39 92.9 33 84.6
UniProt, Literature & Detection 18 18 100.0 11 61.1 UniProt, Literature & Prediction 34 32 94.1 12 37.5 UniProt, Detection & Prediction 30 30 100.0 14 46.7 Literature, Detection & Prediction
24 24 100.0 15 62.5
UniProt & Literature 13 13 100.0 7 53.8 UniProt & Detection 16 16 100.0 11 68.8 UniProt & Prediction 55 47 85.5 15 31.9 Literature & Detection 22 22 100.0 10 45.5 Literature & Prediction 10 10 100.0 4 40.0 Detection & Prediction 40 40 100.0 23 57.5 UniProt only 12 10 83.3 5 50.0 Literature only 10 9 90.0 4 44.4 Detection only 22 22 100.0 17 77.3 Prediction only 40 39 97.5 9 23.1 All with UniProt 220 205 93.2 108 52.7 All with Literature 173 167 96.5 96 57.5 All with Detection 214 211 98.6 134 63.5 All with Prediction 275 261 94.9 125 47.9 Overall 388 371 95.6 190 51.2
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Table S5. MRM assay of individual proteins.
(In a separate file of 277 pages: See (17) for definition of terminologies.)
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Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MXCC05430H11101XMR1B
1 1 HPS HPS NA NA NA NA NA NA NA NA 0.012
MZCO58030H11101XMR1
1 2 IUCPQ 2683 81 Male 10 Past 62.5 Benign Granuloma Necrotizing Granuloma 0.860
MZCO55530H11101XMR1
1 3 IUCPQ 1996 78 Male 10 Past NA Cancer Adenocarcinoma NA 0.371
MZCO59230H11101XMR1
1 4 IUCPQ 2984 77 Male 26 NA 45.6 Benign Hamartoma NA 0.505
MZCO57530H11101XMR1
1 5 IUCPQ 2585 75 Male 9 Past 91.5 Cancer Adenocarcinoma NA 0.915
MZCO55930H11101XMR1
1 6 IUCPQ 2042 56 Female 13 Past 39 Cancer Adenocarcinoma NA 0.857
MZCO58130H11101XMR1
1 7 IUCPQ 2690 61 Female 14 Never 0 Benign Granuloma Necrotizing Granuloma 0.092
MZCO58930H11101XMR1
1 8 IUCPQ 2912 62 Male 13 Past 25 Cancer Adenocarcinoma NA 0.038
MZCO58730H11101XMR1
1 9 IUCPQ 2866 63 Male 10 Current 36 Benign Granuloma Necrotizing Granuloma 0.672
MZCO55630H11101XMR1
1 10 IUCPQ 1999 42 Female 12 Never 0 Benign Hamartoma Hamartoma 0.625
MZCO59030H11101XMR1
1 11 IUCPQ 2918 46 Female 12 Past 35 Cancer Adenocarcinoma NA 0.417
MZCO56330H11101XMR1
1 12 IUCPQ 2196 56 Male 13 Past 47.5 Cancer Adenocarcinoma NA 0.776
MZCO59630H11101XMR1
1 13 IUCPQ 3242 48 Male 13 Current 13.2 Benign Granuloma Necrotizing Granuloma 0.793
MZCO56730H11101XMR1
1 14 IUCPQ 2331 78 Male 9 Past 19.5 Benign Other Pulmonary Infarcct 0.801
MZCO57730H11101XMR1
1 15 IUCPQ 2670 78 Male 12 Past 69 Cancer Adenocarcinoma NA 0.321
Submitted Manuscript: Confidential
72
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MXCC05430H11101XMR5
1 16 HPS HPS NA NA NA NA NA NA NA NA 0.094
MZCO57930H11101XMR1
1 17 IUCPQ 2680 62 Male 40 Past NA Benign Other Hemorraghic Infarct 0.435
MZCO59430H11101XMR1
1 18 IUCPQ 3136 60 Male 12 Past 17.5 Cancer Adenocarcinoma NA 0.732
MZCO58430H11101XMR1
1 19 IUCPQ 2796 64 Male 14 Past 42 Benign Granuloma Necrotizing Granuloma 0.329
MZCO56030H11101XMR1
1 20 IUCPQ 2071 66 Male 13 Past NA Cancer Adenocarcinoma NA 0.834
MZCO56130H11101XMR1
1 21 IUCPQ 2082 47 Female 13 Past 30 Cancer Adenocarcinoma NA 0.981
MZCO59930H11101XMR1
1 22 IUCPQ 3512 52 Female 10 Current 39 Benign Granuloma Necrotizing Granuloma 0.886
MZCO59530H11101XMR1
1 23 IUCPQ 3239 66 Male 12 Current NA Benign Other Fibroelastic Nodule 0.617
MZCO56830H11101XMR1
1 24 IUCPQ 2333 66 Male 18 Past 49 Cancer Adenocarcinoma NA 0.898
MZCO57030H11101XMR1
1 25 IUCPQ 2370 49 Female 10 Current 15 Cancer Adenocarcinoma NA 0.876
MZCO55030H11101XMR1
1 26 IUCPQ 1845 52 Female 9 Past 40 Benign Hamartoma NA 0.483
MZCO57130H11101XMR1
1 27 IUCPQ 2419 65 Male 5 Past 55 Benign Granuloma Necrotizing Granuloma 0.498
MZCO59130H11101XMR1
1 28 IUCPQ 2965 67 Male 10 Past 132.5 Cancer Adenocarcinoma NA 0.971
MZCO58530H11101XMR1
1 29 IUCPQ 2806 55 Male 17 Current 40 Cancer Adenocarcinoma NA 0.871
MZCO58330H11101XMR1
1 30 IUCPQ 2789 47 Male 12 Current 34 Benign Other Amyloidosis 0.148
Submitted Manuscript: Confidential
73
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MXCC05430H11101XMR6
1 31 HPS HPS NA NA NA NA NA NA NA NA 0.041
MXCC05431H11101XMR1
2 1 HPS HPS NA NA NA NA NA NA NA NA 0.039
MZCO53631H11101XMR1
2 2 UPenn 20574 64 Female 39 Past 7.5 Cancer Adenocarcinoma NA 0.789
MZCO48531H11101XMR1
2 3 UPenn 20302 63 Female 35 Never 0 Benign Granuloma NA 0.416
MZCO51831H11101XMR1
2 4 UPenn 20490 63 Female 18 Past 45 Benign Granuloma Necrotizing Granuloma 0.698
MZCO38531H11101XMR1
2 5 UPenn 1416 56 Male 28 Past 40 Cancer Adenocarcinoma NA 0.951
MZCO43031H11101XMR1
2 6 UPenn 20038 65 Female 9 Past 20 Cancer Adenocarcinoma NA 0.433
MZCO51631H11101XMR1
2 7 UPenn 20475 65 Female 7 Never 0 Benign Granuloma Non-necrotizing Granuloma 0.400
MZCO36931H11101XMR1
2 8 UPenn 1289 52 Male 13 Past 50 Benign Granuloma Necrotizing Granuloma 0.570
MZCO54231H11101XMR1
2 9 UPenn 20593 57 Male 9 Past 75 Cancer Adenocarcinoma NA 0.501
MZCO47931H11101XMR1
2 10 UPenn 20281 68 Female 45 Never 0 Cancer Adenocarcinoma NA 0.512
MZCO49831H11101XMR1
2 11 UPenn 20392 70 Female 12 Never 0 Benign Granuloma Necrotizing Granuloma 0.317
MZCO48231H11101XMR1
2 12 UPenn 20290 69 Male 13 Past 60 Benign Other Amyloidosis 0.557
MZCO37731H11101XMR1
2 13 UPenn 1344 69 Male 20 Past 120 Cancer Other Large Cell Squamous Cell 0.548
MZCO53131H11101XMR1
2 14 UPenn 20544 77 Female 13 Never 0 Cancer Adenocarcinoma NA 0.788
Submitted Manuscript: Confidential
74
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO42231H11101XMR1
2 15 UPenn 1755 77 Female 20 Past 8.6 Benign Scar NA 0.821
MXCC05431H11101XMR2
2 16 HPS HPS NA NA NA NA NA NA NA NA 0.098
MZCO45131H11101XMR1
2 17 UPenn 20150 44 Female 11.6 Past 6 Benign Hamartoma Hamartoma 0.059
MZCO38831H11101XMR1
2 18 UPenn 1430 62 Female 12 Past 94 Cancer Adenocarcinoma NA 0.841
MZCO38431H11101XMR1
2 19 UPenn 1403 68 Male 14 Past 4.5 Cancer Mixed NA 0.909
MZCO49931H11101XMR1
2 20 UPenn 20403 72 Male 1.5 Past 15 Benign Granuloma Necrotizing Granuloma 0.510
MZCO46031H11101XMR1
2 21 UPenn 20172 61 Female 12 Past 30 Cancer Adenocarcinoma NA 0.893
MZCO37131H11101XMR1
2 22 UPenn 1305 57 Female 10 Past 20 Benign Granuloma NA 0.018
MZCO47431H11101XMR1
2 23 UPenn 20250 44 Male 15 Past 45 Benign Hamartoma NA 0.289
MZCO39231H11101XMR1
2 24 UPenn 1436 54 Male 13 Past 54 Cancer Adenocarcinoma NA 0.705
MZCO44031H11101XMR1
2 25 UPenn 20109 60 Female 14 Past 30 Cancer Adenocarcinoma NA 0.817
MZCO37231H11101XMR1
2 26 UPenn 1309 57 Female 30 NA 60 Benign Other Subpleural Fibrosis Benign Lymphoid Hyperplasia
0.553
MZCO40531H11101XMR1
2 27 UPenn 1488 77 Male 17 Past 17.5 Benign Granuloma NA 0.774
MZCO43431H11101XMR1
2 28 UPenn 20069 77 Male 13 Past 12 Cancer Mixed NA 0.814
MZCO49131H11101XMR1
2 29 UPenn 20325 64 Female 9 Current 50 Cancer Adenocarcinoma NA 0.597
Submitted Manuscript: Confidential
75
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO41531H11101XMR1
2 30 UPenn 1594 70 Female 14 Past 20 Benign Granuloma Necrotizing Granuloma 0.672
MZCO45531H11101XMR1
2 31 UPenn 20155 59 Female 15 Past 40 Cancer Adenocarcinoma NA 0.892
MZCO46431H11101XMR1
2 32 UPenn 20183 56 Female 16 Never 0 Benign Hamartoma NA 0.334
MXCC05431H11101XMR3
2 33 HPS HPS NA NA NA NA NA NA NA NA 0.080
MXCC05401I11101XMR1
3 1 HPS HPS NA NA NA NA NA NA NA NA 0.141
MZCO42101I11101XMR1
3 2 UPenn 1753 48 Female 13 Past 22.5 Benign Granuloma NA 0.056
MZCO45201I11101XMR1
3 3 UPenn 20151 64 Female 6 Never 0 Cancer Adenocarcinoma NA 0.645
MZCO37001I11101XMR1
3 4 UPenn 1297 69 Female 14 Past 40 Cancer Squamous NA 0.844
MZCO52501I11101XMR1
3 5 UPenn 20519 74 Female 4 Past NA Benign Other Organizing Pneumonia 0.861
MZCO47201I11101XMR1
3 6 UPenn 20239 60 Male 13 Current 40 Benign Granuloma Necrotizing Granuloma 0.392
MZCO52901I11101XMR1
3 7 UPenn 20529 61 Male 12 Past 17.5 Cancer Other Adenocarcinoma Squamous 0.879
MZCO44501I11101XMR1
3 8 UPenn 20124 68 Female 16 Past 60 Cancer Adenocarcinoma NA 0.828
MZCO52601I11101XMR1
3 9 UPenn 20524 67 Female 12 Never 0 Benign Granuloma Necrotizing Granuloma 0.273
MZCO45701I11101XMR1
3 10 UPenn 20166 59 Male 13 Past 40.5 Benign Granuloma NA 0.204
MZCO46301I11101XMR1
3 11 UPenn 20181 72 Male 21 Past 25 Cancer Squamous NA 0.790
Submitted Manuscript: Confidential
76
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO36801I11101XMR1
3 12 UPenn 1287 53 Female 13 Past 20 Cancer Adenocarcinoma NA 0.122
MZCO51301I11101XMR1
3 13 UPenn 20468 51 Female 15 Past 32 Benign Granuloma Necrotizing Granuloma 0.366
MZCO41601I11101XMR1
3 14 UPenn 1627 50 Female 6 Past 20 Benign Scar NA 0.261
MZCO52001I11101XMR1
3 15 UPenn 20507 51 Female 27 Past 40 Cancer Squamous NA 0.455
MXCC05401I11101XMR2
3 16 HPS HPS NA NA NA NA NA NA NA NA 0.106
MZCO49501I11101XMR1
3 17 UPenn 20376 63 Male 22 Past 45 Cancer Adenocarcinoma NA 0.899
MZCO36401I11101XMR1
3 18 UPenn 1257 50 Male 19 Past 30 Benign Hamartoma NA 0.807
MZCO53801I11101XMR1
3 19 UPenn 20578 70 Female 12 Past 55 Benign Granuloma Necrotizing Granuloma 0.926
MZCO49001I11101XMR1
3 20 UPenn 20314 71 Female 12 Past 80 Cancer Adenocarcinoma NA 0.602
MZCO41801I11101XMR1
3 21 UPenn 1748 66 Female 6 Past 8 Benign Other Lymphoid Aggregate 0.760
MZCO49401I11101XMR1
3 22 UPenn 20369 68 Female 9 Past 28 Cancer Adenocarcinoma NA 0.854
MZCO50901I11101XMR1
3 23 UPenn 20450 46 Male 13 Past 32 Cancer Adenocarcinoma NA 0.724
MZCO47801I11101XMR1
3 24 UPenn 20277 45 Male 11 Past 2.55 Benign Granuloma Necrotizing Granuloma 0.283
MZCO40101I11101XMR1
3 25 UPenn 1469 66 Female 15 Past 16 Cancer Adenocarcinoma NA 0.803
MZCO54401I11101XMR1
3 26 UPenn 20612 57 Female 17 Past 10 Benign Granuloma Necrotizing Granuloma 0.491
Submitted Manuscript: Confidential
77
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO46701I11101XMR1
3 27 UPenn 20205 85 Female 15 Never 0 Benign Granuloma NA 0.291
MZCO41401I11101XMR1
3 28 UPenn 1572 77 Female 20 NA 15 Cancer Other not specified 0.992
MZCO43601I11101XMR1
3 29 UPenn 20081 71 Male 6 Past 25 Cancer Adenocarcinoma NA 0.874
MZCO48901I11101XMR1
3 30 UPenn 20312 69 Male 33 Past 98 Benign Granuloma NA 0.486
MXCC05401I11101XMR3
3 31 HPS HPS NA NA NA NA NA NA NA NA 0.312
MXCC05402I11101XMR4
4 1 HPS HPS NA NA NA NA NA NA NA NA 0.485
MZCO66902I11101XMR1
4 2 NYU NYU187 64 Female 23 Past 35 Benign Granuloma Necrotizing Granuloma 0.299
MZCO60102I11101XMR1
4 3 NYU NYU16 52 Female 18 Past 30 Cancer Mixed NA 0.949
MZCO60602I11101XMR1
4 4 NYU NYU173 80 Female 12 Never 0 Benign Granuloma NA 0.378
MZCO64902I11101XMR1
4 5 NYU NYU646 79 Female 21 Past NA Cancer Mixed NA 0.704
MZCO69102I11101XMR1
4 6 NYU NYU1176 73 Male 8 Past 100 Cancer Mixed Mixed Adeno BAC 0.820
MZCO61502I11101XMR1
4 7 NYU NYU514 67 Male 10 Past 30 Benign Granuloma Necrotizing Granuloma 0.605
MZCO71202I11101XMR1
4 8 NYU NYU1096 58 Female 17 Past 10 Cancer Adenocarcinoma NA 0.579
MZCO69002I11101XMR1
4 9 NYU NYU1183 53 Female 14 Never 0 Benign Granuloma Necrotizing Granuloma 0.112
MZCO67602I11101XMR1
4 10 NYU NYU841 68 Female 15 Past 40 Benign Granuloma Necrotizing Granuloma 0.667
Submitted Manuscript: Confidential
78
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO61702I11101XMR1
4 11 NYU NYU112 72 Female 24 Past 50 Cancer Adenocarcinoma NA 0.636
MZCO61802I11101XMR1
4 12 NYU NYU111 60 Male 10 Past 30 Cancer BAC NA 0.833
MZCO64302I11101XMR1
4 13 NYU NYU453 67 Male 18 Past 40 Benign Granuloma Necrotizing Granuloma 0.614
MZCO66802I11101XMR1
4 14 NYU NYU1240S 47 Female 16 Past 30 Benign Granuloma NA 0.064
MZCO60202I11101XMR1
4 15 NYU NYU268 48 Female 12 Current 30 Cancer Mixed NA 0.841
MXCC05402I11101XMR5
4 16 HPS HPS NA NA NA NA NA NA NA NA 0.051
MZCO62302I11101XMR1
4 17 NYU NYU1317S 60 Female 8 Past 40 Cancer Mixed Mixed Adeno BAC 0.896
MZCO70402I11101XMR1
4 18 NYU NYU986 37 Female 9 Never 0 Benign Other Fibrosis 0.193
MZCO66202I11101XMR1
4 19 NYU NYU509 52 Male 25 Past 35 Benign Granuloma Necrotizing Granuloma 0.181
MZCO67202I11101XMR1
4 20 NYU NYU875 54 Male 13 Past 60 Cancer Mixed NA 0.867
MZCO71402I11101XMR1
4 21 NYU NYU907 78 Female 13 Past 60 Cancer Other Pleomorphic Carcinoma 0.902
MZCO62102I11101XMR1
4 22 NYU NYU332 80 Female 13 Past 30 Benign Hamartoma NA 0.597
MZCO69302I11101XMR1
4 23 NYU NYU1145 70 Female 10 Past 3.5 Benign Other Sclerosing Hemangioma 0.313
MZCO65002I11101XMR1
4 24 NYU NYU379 70 Female 10 Past 45 Cancer Adenocarcinoma NA 0.543
MZCO63802I11101XMR1
4 25 NYU NYU184 77 Male 11 Past 30 Cancer Mixed Mixed Adeno BAC 0.818
Submitted Manuscript: Confidential
79
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO70202I11101XMR1
4 26 NYU NYU1001 86 Male 9 Never 0 Benign Granuloma Necrotizing Granuloma 0.770
MZCO61902I11101XMR1
4 27 NYU NYU92 51 Female 21 Never 0 Cancer Mixed NA 0.894
MZCO63102I11101XMR1
4 28 NYU NYU24 51 Female 13 Never 0 Benign Hamartoma NA 0.478
MZCO61002I11101XMR1
4 29 NYU NYU84 55 Female 19 Past NA Benign Granuloma Non-necrotizing Granuloma 0.764
MZCO63902I11101XMR1
4 30 NYU NYU697S 65 Female 8 Current 30 Cancer Mixed Mixed Adeno BAC 0.660
MXCC05402I11101XMR6A
4 31 HPS HPS NA NA NA NA NA NA NA NA 0.491
MXCC05403I11101XMR1
5 1 HPS HPS NA NA NA NA NA NA NA NA 0.101
MZCO69203I11101XMR1
5 2 NYU NYU1168 79 Female 10 Never 0 Benign Granuloma Necrotizing Granuloma 0.740
MZCO64403I11101XMR1
5 3 NYU NYU661 79 Female 10 Never 0 Cancer Mixed Mixed Adeno BAC 0.603
MZCO61403I11101XMR1
5 4 NYU NYU513 66 Female 10 Never 0 Benign Granuloma Non-necrotizing Granuloma 0.459
MZCO65103I11101XMR1
5 5 NYU NYU613S 64 Female 10 Past 40 Cancer Mixed Mixed Adeno BAC 0.713
MZCO71103I11101XMR1
5 6 NYU NYU1141 63 Male 10 Past 20 Cancer Mixed Mixed Adeno BAC 0.885
MZCO64603I11101XMR1
5 7 NYU NYU423 63 Male 8 Past 30 Benign Granuloma Necrotizing Granuloma 0.341
MZCO69703I11101XMR1
5 8 NYU NYU1098 67 Female 9 Past 80 Benign Other Organizing Pneumonia 0.859
MZCO65303I11101XMR1
5 9 NYU NYU636 67 Female 8 Past 10 Cancer BAC NA 0.928
Submitted Manuscript: Confidential
80
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO63403I11101XMR1
5 10 NYU NYU71 84 Female 12 Never 0 Benign Granuloma Necrotizing Granuloma 0.143
MZCO68003I11101XMR1
5 11 NYU NYU831 83 Female 13 Past 75 Cancer Adenocarcinoma NA 0.748
MZCO66303I11101XMR1
5 12 NYU NYU410 75 Male 14 Past 100 Cancer Mixed NA 0.933
MZCO62403I11101XMR1
5 13 NYU NYU281 73 Male 19 Past 70.5 Benign Granuloma NA 0.288
MZCO68203I11101XMR1
5 14 NYU NYU819 67 Female 43 Never 0 Benign Granuloma NA 0.024
MZCO61603I11101XMR1
5 15 NYU NYU626 68 Female 15 Past 40 Cancer Mixed NA 0.937
MXCC05403I11101XMR2
5 16 HPS HPS NA NA NA NA NA NA NA NA 0.039
MZCO68903I11101XMR1
5 17 NYU NYU1559S 66 Female 13 Past 40 Cancer Mixed NA 0.965
MZCO64703I11101XMR1
5 18 NYU NYU500 49 Female 10 Never 0 Benign Granuloma Necrotizing Granuloma 0.443
MZCO60403I11101XMR1
5 19 NYU NYU209 57 Female 21 Past 36 Benign Granuloma NA 0.406
MZCO64003I11101XMR1
5 20 NYU NYU696 57 Female 15 Past 6 Cancer Mixed NA 0.904
MZCO62203I11101XMR1
5 21 NYU NYU349 72 Male 9 Past 65 Cancer Mixed Mixed Adeno BAC 0.735
MZCO70703I11101XMR1
5 22 NYU NYU968 72 Male 16 Past 8 Benign Granuloma NA 0.248
MZCO62503I11101XMR1
5 23 NYU NYU566 72 Female 23 Past NA Benign Granuloma NA 0.474
MZCO63703I11101XMR1
5 24 NYU NYU46 69 Female 13 Past 40 Cancer BAC NA 0.966
Submitted Manuscript: Confidential
81
Table S6. Experimental design of the discovery study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZCO67703I11101XMR1
5 25 NYU NYU830 60 Female 13 Past NA Cancer Mixed NA 0.805
MZCO66003I11101XMR1
5 27 NYU NYU440 75 Male 10 Past 7.5 Benign Granuloma Necrotizing Granuloma 0.939
MZCO61203I11101XMR1
5 28 NYU NYU560 78 Male 16 Current 120 Cancer Adenocarcinoma NA 0.943
MZCO67003I11101XMR1
5 29 NYU NYU912 64 Female 39 Never 0 Benign Other Organizing Pneumonia 0.670
MZCO71303I11101XMR1
5 30 NYU NYU703 65 Female 17 Past 25 Cancer Mixed NA 0.899
MZCO65903I11101XMR1
5 31 NYU NYU427 72 Female 8 Past 60 Cancer Adenocarcinoma NA 0.728
MZCO63303I11101XMR1
5 32 NYU NYU65 71 Female 30 Past NA Benign Granuloma NA 0.213
MXCC05403I11101XMR3
5 33 HPS HPS NA NA NA NA NA NA NA NA 0.207
Note:
• Sample name: Sample identifier
• Batch: Experimental batch
• Position: Sample position in the batch
• Site
o Participating study sites: IUCPQ (Institut Universitaire de Cardiologie et de Pneumologie de Quebec), NYU (New
York University), UPenn (University of Pennsylvania), and Vanderbilt (Vanderbilt University). HPS (human
plasma standard) samples are also listed.
• Subject: Unique subject identifier by study site.
• Age: Age of patient
Submitted Manuscript: Confidential
82
• Gender: Female/Male
• Nodule size (mm): Radiological nodule size.
• Smoking status: Never/Former/Current
• Smoking pack-years: Smoking history pack-years.
• Disease status: Benign/Cancer
• Histology subgroup
o Benign – Granuloma, Hamartoma, Scar, Other.
o Cancer – Adenocarcinoma, Squamous, Large Cell, BAC, Mixed, Other.
• Histology specific: Specific histology
• Classifier score: Score by the 13-protein lung nodule classifier.
Submitted Manuscript: Confidential
83
Table S7. List of 36 cooperative proteins.
Cat
egor
y
Pro
tein
(H
UM
AN
)
Off
icia
l gen
e na
me
Coo
pera
tive
sc
ore
Par
tial
AU
C
Coe
ffic
ient
CV
Fre
quen
cy
Tra
nsit
ion
for
quan
tita
tion
P v
alue
(M
ann-
Whi
tney
tes
t)
Tra
nsit
ion
for
qual
ific
atio
n
Pep
tide
Q
valu
e
Tis
sue
cand
idat
e
Pre
dict
ed
Con
cent
rati
on
(ng/
ml)
Classifier TSP1 THBS1 1.8 0.25 0.24 59 GFLLLASLR_495.31_559.40
0.23 GFLLLASLR_495.31_318.20
1.90E-05 510
Classifier COIA1 COL18A1 3.7 0.16 0.25 91 AVGLAGTFR_446.26_721.40
0.16 AVGLAGTFR_446.26_551.30
6.70E-04 35
Classifier ISLR ISLR 1.4 0.32 0.25 64 ALPGTPVASSQPR_640.85_841.50
0.74 ALPGTPVASSQPR_640.85_440.30
4.40E-03 -
Classifier TETN CLEC3B 2.5 0.26 0.26 67 LDTLAQEVALLK_657.39_330.20
0.14 LDTLAQEVALLK_657.39_871.50
3.70E-05 58000
Classifier FRIL FTL 2.8 0.31 0.26 53 LGGPEAGLGEYLFER_804.40_913.40
0.19 LGGPEAGLGEYLFER_804.40_525.30
4.30E-05 Secreted, EPI, ENDO
12
Classifier GRP78 HSPA5 1.4 0.27 0.27 40 TWNDPSVQQDIK_715.85_260.20
0.44 TWNDPSVQQDIK_715.85_288.10
1.80E-03 Secreted, EPI, ENDO
100
Classifier ALDOA ALDOA 1.3 0.26 0.28 88 ALQASALK_401.25_617.40
0.57 ALQASALK_401.25_489.30
3.70E-05 Secreted, EPI
250
Classifier BGH3 TGFBI 1.8 0.21 0.28 69 LTLLAPLNSVFK_658.40_804.50
0.57 LTLLAPLNSVFK_658.40_875.50
1.40E-04 140
Classifier LG3BP LGALS3BP 4.3 0.29 0.29 76 VEIFYR_413.73_598.30 0.45 VEIFYR_413.73_485.30 2.80E-05 Secreted 440 Classifier LRP1 LRP1 4.0 0.13 0.32 93 TVLWPNGLSLDIPAG
R_855.00_400.20 0.26 TVLWPNGLSLDIPAGR
_855.00_605.30 1.40E-04 EPI 20
Classifier FIBA FGA 1.1 0.31 0.35 11 NSLFEYQK_514.76_714.30
0.57 NSLFEYQK_514.76_315.20
1.90E-05 130000
Classifier PRDX1 PRDX1 1.5 0.32 0.37 68 QITVNDLPVGR_606.30_428.30
0.24 QITVNDLPVGR_606.30_770.40
1.90E-05 EPI 60
Classifier GSLG1 GLG1 1.2 0.34 0.45 23 IIIQESALDYR_660.86_338.20
0.27 IIIQESALDYR_660.86_724.40
6.70E-03 EPI, ENDO
-
Robust KIT KIT 1.4 0.33 0.46 28 YVSELHLTR_373.21_263.10
0.27 YVSELHLTR_373.21_526.30
2.40E-03 8.2
Submitted Manuscript: Confidential
84
Table S7. List of 36 cooperative proteins.
Cat
egor
y
Pro
tein
(H
UM
AN
)
Off
icia
l gen
e na
me
Coo
pera
tive
sc
ore
Par
tial
AU
C
Coe
ffic
ient
CV
Fre
quen
cy
Tra
nsit
ion
for
quan
tita
tion
P v
alue
(M
ann-
Whi
tney
tes
t)
Tra
nsit
ion
for
qual
ific
atio
n
Pep
tide
Q
valu
e
Tis
sue
cand
idat
e
Pre
dict
ed
Con
cent
rati
on
(ng/
ml)
Robust CD14 CD14 4.0 0.33 0.48 73 ATVNPSAPR_456.80_527.30
0.72 ATVNPSAPR_456.80_386.20
4.30E-04 EPI 420
Robust EF1A1 EEF1A1 1.2 0.32 0.56 52 IGGIGTVPVGR_513.30_428.30
0.53 IGGIGTVPVGR_513.30_628.40
4.50E-04 Secreted, EPI
61
Robust TENX TNXB 1.1 0.30 0.56 22 YEVTVVSVR_526.29_759.50
0.54 YEVTVVSVR_526.29_660.40
1.10E-03 ENDO 70
Robust AIFM1 AIFM1 1.4 0.32 0.70 6 ELWFSDDPNVTK_725.85_558.30
0.20 ELWFSDDPNVTK_725.85_875.40
3.70E-02 EPI, ENDO
1.4
Robust GGH GGH 1.3 0.32 0.81 43 YYIAASYVK_539.28_638.40
0.24 YYIAASYVK_539.28_567.30
1.70E-03 250
Robust IBP3 IGFBP3 3.4 0.32 1.82 58 FLNVLSPR_473.28_685.40
0.04 FLNVLSPR_473.28_359.20
2.80E-05 5700
Robust ENPL HSP90B1 1.1 0.29 5.90 22 SGYLLPDTK_497.27_460.20
0.57 SGYLLPDTK_497.27_573.30
1.10E-03 Secreted, EPI, ENDO
88
Non-Robust
ERO1A ERO1L 6.2 VLPFFERPDFQLFTGNK_685.70_318.20
0.06 VLPFFERPDFQLFTGNK_685.70_419.20
1.20E-02 Secreted, EPI, ENDO
-
Non-Robust
6PGD PGD 4.3 LVPLLDTGDIIIDGGNSEYR_1080.60_897.40
0.03 LVPLLDTGDIIIDGGNSEYR_1080.60_974.50
5.50E-03 EPI, ENDO
29
Non-Robust
ICAM1 ICAM1 3.9 VELAPLPSWQPVGK_760.93_342.20
0.31 VELAPLPSWQPVGK_760.93_413.20
2.80E-02 71
Non-Robust
PTPA PPP2R4 2.1 FGSLLPIHPVTSG_662.87_807.40
0.26 FGSLLPIHPVTSG_662.87_292.10
1.90E-03 ENDO 3.3
Non-Robust
NCF4 NCF4 2.0 GATGIFPLSFVK_618.85_837.50
0.11 GATGIFPLSFVK_618.85_690.40
7.90E-04 ENDO -
Non-Robust
SEM3G SEMA3G 1.9 LFLGGLDALYSLR_719.41_837.40
0.20 LFLGGLDALYSLR_719.41_538.30
1.10E-03 -
Submitted Manuscript: Confidential
85
Table S7. List of 36 cooperative proteins.
Cat
egor
y
Pro
tein
(H
UM
AN
)
Off
icia
l gen
e na
me
Coo
pera
tive
sc
ore
Par
tial
AU
C
Coe
ffic
ient
CV
Fre
quen
cy
Tra
nsit
ion
for
quan
tita
tion
P v
alue
(M
ann-
Whi
tney
tes
t)
Tra
nsit
ion
for
qual
ific
atio
n
Pep
tide
Q
valu
e
Tis
sue
cand
idat
e
Pre
dict
ed
Con
cent
rati
on
(ng/
ml)
Non-Robust
1433T YWHAQ 1.5 TAFDEAIAELDTLNEDSYK_1073.00_748.40
0.69 TAFDEAIAELDTLNEDSYK_1073.00_969.50
1.10E-02 EPI 180
Non-Robust
RAP2B RAP2B 1.5 VDLEGER_409.21_603.30
0.34 VDLEGER_409.21_361.20
1.20E-03 EPI -
Non-Robust
MMP9 MMP9 1.4 AFALWSAVTPLTFTR_840.96_290.20
0.36 AFALWSAVTPLTFTR_840.96_589.30
4.00E-03 28
Non-Robust
FOLH1 FOLH1 1.3 LGSGNDFEVFFQR_758.37_825.40
0.06 LGSGNDFEVFFQR_758.37_597.30
5.80E-03 -
Non-Robust
GSTP1 GSTP1 1.3 ALPGQLKPFETLLSQNQGGK_709.39_831.40
0.46 ALPGQLKPFETLLSQNQGGK_709.39_261.20
1.70E-04 ENDO 32
Non-Robust
EF2 EEF2 1.3 FSVSPVVR_445.76_470.30
0.79 FSVSPVVR_445.76_557.30
1.10E-02 Secreted, EPI
30
Non-Robust
RAN RAN 1.2 LVLVGDGGTGK_508.29_591.30
0.27 LVLVGDGGTGK_508.29_326.20
2.80E-03 Secreted, EPI
4.6
Non-Robust
SODM SOD2 1.2 NVRPDYLK_335.52_260.20
0.86 NVRPDYLK_335.52_423.30
2.40E-02 Secreted 7.1
Non-Robust
DSG2 DSG2 1.1 GQIIGNFQAFDEDTGLPAHAR_753.04_299.20
0.08 GQIIGNFQAFDEDTGLPAHAR_753.04_551.30
5.70E-03 ENDO 2.7
Note:
• Category o Classifier: The protein belongs to the 13-protein classifier. o Robust: The protein is a cooperative protein with robust signal. o Non-Robust: The protein is a cooperative protein but with noisy signal or having interference.
• Protein (_HUMAN): UniProt protein name • Official gene name: Entrez gene symbol
Submitted Manuscript: Confidential
86
• Cooperative score: The ratio between the occurrences of the protein in the top 100 panels and the expected occurrences by chance alone.
• Partial AUC: The partial area under the receiver operating characteristic (ROC) curve (AUC) (37, 68) of the classifier just before the protein was removed from the classifier.
• Coefficient CV: The coefficient of variation (CV) of the logistic regression coefficient just before the protein was removed from the classifier.
• Frequency: How many times the protein occurred in the top 100 panels out of all possible panels of the 21 robust cooperative proteins.
• Transition for quantitation: The transition (quantifier) used for measuring protein abundance in samples. It is the transition having the highest median intensity among all transitions of the protein.
• P value (Mann-Whitney test): The p value of the quantifier transition in distinguishing cancer vs. benign samples, based on Mann-Whitney test (31).
• Transition for qualification: The transition (together with the quantifier transition) used for calculating peptide q value. It is also the transition having the second highest median intensity among all transitions of the peptide.
• Peptide Q value: Peptide q value: See Supplementary Materials and Methods for more details. • Tissue candidate: Whether the protein was selected as a tissue biomarker candidate: See Table S3. • Predicted Concentration (ng/ml): Protein concentration in blood (69).
Submitted Manuscript: Confidential
87
Table S8. Results from logistic regression diagnostics.
Diagnostics Results Discussion Model specification Linear predicted value: p < 0.001
Linear predicted value squared: p = 0.11
The model had relevant predictors and their linear combination was a sufficient predictor.
Goodness-of-fit
(Hosmer-Lemeshow
chi-square)
p = 0.82 The model fitted the data well.
Collinearity The lowest tolerance was 0.39 and the highest variance inflation factor (VIF) was 2.54.
No obvious collinearity was observed.
Influential observations
Standardized Pearson residual: 11 samples had an absolute value greater than 2.
Deviance residual: 2 samples had an absolute value greater than 2.
Leverage: No sample had a value greater than 3 times of the average.
Using the step-down Šidák procedure (71) to control multiple testing error (α=0.05), there were three outlier samples by the standardized Pearson residual method and none by the deviance residual method. Combining all evidence, it is inconclusive whether there were outlier samples in the dataset.
A logistic regression model was fitted to the whole discovery dataset. Technical details can be found in (35, 70).
Submitted Manuscript: Confidential
88
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
Validation Set 1 MXCC05430H11101XMR1 1 1 HPS HPS NA NA NA NA NA NA NA NA 0.247 MZCO54930H11101XMR1 1 3 IUCPQ 1842 74 Female 19 Current 50 Cancer Squamous NA 0.858 MZCO56430H11101XMR1 1 4 IUCPQ 2222 62 Male 19 Current 70.5 Cancer Squamous NA 0.915 MZCO56630H11101XMR1 1 5 IUCPQ 2324 62 Male 24 Past 50 Benign Other
Fibrotic Inflammatory Lesion 0.892
MZCO58230H11101XMR1 1 6 IUCPQ 2788 58 Female 10 Past 45 Cancer Mixed NA 0.701 MZCO57830H11101XMR1 1 7 IUCPQ 2676 58 Female 15 Past 129 Benign Scar NA 0.779 MZCO55330H11101XMR1 1 8 IUCPQ 1955 36 Female 12 Current 10.5 Benign Other Lymphangioma 0.737 MZCO57430H11101XMR1 1 9 IUCPQ 2475 64 Female 10 Past 33.75 Cancer Adenocarcinoma NA 0.144 MZCO59330H11101XMR1 1 10 IUCPQ 3076 68 Male 20 Past 40 Benign Hamartoma NA 0.085 MZCO55430H11101XMR1 1 11 IUCPQ 1958 68 Male 14 Past 56 Cancer Adenocarcinoma NA 0.437 MZCO57330H11101XMR1 1 14 IUCPQ 2450 62 Female 23 Past NA Benign Other Pulmonary Infarct 0.678 MZCO56230H11101XMR1 1 15 IUCPQ 2116 58 Female 22 Current 19 Cancer Mixed NA 0.790 MXCC05430H11101XMR2 1 16 HPS HPS NA NA NA NA NA NA NA NA 0.116 MZCO55130H11101XMR1 1 26 IUCPQ 1871 64 Female 26 Never 0 Benign Granuloma Necrotizing Granuloma 0.850 MXCC05430H 1 29 HPS HPS NA NA NA NA NA NA NA NA 0.259
Submitted Manuscript: Confidential
89
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
11101XMR1A MXCC05431H11101XMR4 2 1 HPS HPS NA NA NA NA NA NA NA NA 0.039 MZCO46231H11101XMR1 2 2 UPenn 20177 68 Male 26 Past 78 Benign Granuloma NA 0.090 MZCO41731H11101XMR1 2 3 UPenn 1692 72 Male 15 Past 100 Cancer Squamous NA 0.863 MZCO43131H11101XMR1 2 4 UPenn 20039 57 Male 30 Past 40 Cancer Adenocarcinoma NA 0.437 MZCO38231H11101XMR1 2 5 UPenn 1399 58 Male 25 Current 40 Benign Granuloma NA 0.759 MZCO53331H11101XMR1 2 7 UPenn 20548 75 Female 14 Past 15.5 Cancer Adenocarcinoma NA 0.783 MZCO45931H11101XMR1 2 9 UPenn 20171 83 Male 14 Never 0 Benign Granuloma Necrotizing Granuloma 0.982 MZCO53731H11101XMR1 2 10 UPenn 20576 55 Male 22 Past 15 Benign Hamartoma NA 0.897 MXCC05431H11101XMR5 2 12 HPS HPS NA NA NA NA NA NA NA NA 0.106 MZCO36131H11101XMR1 2 14 UPenn 1238 59 Female 16 Past 30 Cancer Adenocarcinoma NA 0.616 MZCO44831H11101XMR1 2 16 UPenn 20144 66 Male 19 Past 45 Cancer Squamous NA 0.583 MZCO41231H11101XMR1 2 17 UPenn 1553 61 Female 19 Past 40 Cancer Adenocarcinoma NA 0.617 MZCO48031H11101XMR1 2 18 UPenn 20283 36 Female 21 Past 3.5 Benign Hamartoma NA 0.212 MZCO53931H11101XMR1 2 19 UPenn 20581 49 Male 18 Past 30 Cancer Squamous NA 0.815 MXCC05431H 2 23 HPS HPS NA NA NA NA NA NA NA NA 0.060
Submitted Manuscript: Confidential
90
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
11101XMR6 MXCC05401I11101XMR4 3 1 HPS HPS NA NA NA NA NA NA NA NA 0.052 MZCO62001I11101XMR1 3 2 NYU NYU330 71 Female 20 Past NA Cancer Mixed NA 0.504 MZCO67501I11101XMR1 3 3 NYU NYU862 68 Female 17 Past 52 Benign Granuloma Necrotizing Granuloma 0.480 MZCO69601I11101XMR1 3 4 NYU NYU1117 65 Male 24 Past 30 Benign Granuloma NA 0.970 MZCO68501I11101XMR1 3 6 NYU NYU777 60 Female 25 Current 90 Cancer Mixed NA 0.531 MZCO63201I11101XMR1 3 8 NYU NYU28 64 Female 13 Past NA Benign Granuloma Necrotizing Granuloma 0.615 MZCO64201I11101XMR1 3 12 NYU NYU457 74 Female 20 Never 0 Cancer Mixed NA 0.484 MZCO62601I11101XMR1 3 13 NYU NYU533 84 Female 21 Never 0 Benign Granuloma Necrotizing Granuloma 0.612 MZCO60701I11101XMR1 3 15 NYU NYU176 38 Female 22 Never 0 Benign Granuloma Necrotizing Granuloma 0.629 MXCC05401I11101XMR5 3 16 HPS HPS NA NA NA NA NA NA NA NA 0.280 MZCO70501I11101XMR1 3 17 NYU NYU974 77 Male 15 Past NA Benign Granuloma NA 0.547 MZCO60501I11101XMR1 3 18 NYU NYU293 77 Male 20 Current 160 Cancer Squamous NA 0.898 MZCO62901I11101XMR1 3 20 NYU NYU575 61 Female 27 Past 40 Cancer Adenocarcinoma NA 0.340 MZCO68101I11101XMR1 3 22 NYU NYU815 52 Female 24 Past 15 Benign Hamartoma NA 0.133 MZCO66501I1 3 25 NYU NYU409 60 Female 12 NA 60 Benign Hamartoma NA 0.086
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91
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
1101XMR1A MZCO69801I11101XMR1 3 29 NYU NYU1044 52 Male 14 Current 30 Cancer Squamous NA 0.960 MZCO62801I11101XMR1 3 31 NYU NYU144 54 Female 5 Past 20 Benign Other Respiratory Bronchiolitis 0.119 MXCC05401I11101XMR6 3 33 HPS HPS NA NA NA NA NA NA NA NA 0.175 MXCC05402I11101XMR1 4 1 HPS HPS NA NA NA NA NA NA NA NA 0.090 MZCO40602I11101XMR1 4 4 UPenn 1490 74 Male 22 Never 0 Benign Other Organizing Pneumonia 0.916 MZCO51702I11101XMR1 4 6 UPenn 20488 57 Female 19 Past 18.5 Cancer Adenocarcinoma NA 0.243 MZCO39602I11101XMR1 4 7 UPenn 1450 58 Female 13 Current 40 Benign Granuloma Necrotizing Granuloma 0.940 MZCO41002I11101XMR1 4 8 UPenn 1527 58 Male 18 Past 102 Benign Granuloma Necrotizing Granuloma 0.483 MZCO41902I11101XMR1 4 9 UPenn 1750 62 Male 25 Past 75 Cancer Other Large Cell Squamous Cell 0.919 MZCO37402I11101XMR1 4 10 UPenn 1328 54 Male 24 Never 0 Benign Scar NA 0.988 MZCO36502I11101XMR1 4 11 UPenn 1266 61 Male 16 Past 60 Cancer Adenocarcinoma NA 0.779 MXCC05402I11101XMR2 4 12 HPS HPS NA NA NA NA NA NA NA NA 0.067 MZCO44102I11101XMR1 4 13 UPenn 20119 67 Female 18 Past 27 Benign Granuloma Necrotizing Granuloma 0.921 MZCO40702I11101XMR1 4 14 UPenn 1492 75 Female 10 Current 25 Cancer Squamous NA 0.372 MZCO47502I1 4 16 UPenn 20251 56 Male 26 Past 10 Benign Other Intussusception 0.042
Submitted Manuscript: Confidential
92
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
1101XMR1 MZCO46902I11101XMR1 4 17 UPenn 20222 65 Male 25 Past 43 Benign Other Lymphocytes Histiocytes 0.830 MZCO51102I11101XMR1 4 18 UPenn 20454 62 Male 23 Past 23.5 Cancer Squamous NA 0.754 MZCO39702I11101XMR1 4 21 UPenn 1452 63 Male 20 Past 20 Cancer Adenocarcinoma NA 0.872 MZCO39902I11101XMR1 4 22 UPenn 1462 65 Male 25 Past 50 Benign Granuloma Necrotizing Granuloma 0.835 MZCO50302I11101XMR1 4 23 UPenn 20434 62 Male 24 Current 92 Cancer Squamous NA 0.789 MXCC05402I11101XMR3 4 25 HPS HPS NA NA NA NA NA NA NA NA 0.023 Validation Set 2 MXCC05426E12101XMR1 1 1 HPS HPS NA NA NA NA NA NA NA NA 0.071 MZEB33326E12101XMR1 1 2
Vanderbilt 7517 74 Male 14 Past 100 Cancer Squamous NA 0.451
MZEB32226E12101XMR1 1 3
Vanderbilt 7320 71 Female 10 Current 100 Benign Other Bronchial Epithelial Cells 0.591
MZEB35726E12101XMR1 1 4
Vanderbilt 8339 62 Female 16 Never 0 Benign Granuloma Necrotizing Granuloma 0.737
MZEB32926E12101XMR1 1 5
Vanderbilt 7476 56 Female 12 Past 5 Cancer Other Carcinoid 0.598
MZEB33426E12101XMR1 1 6
Vanderbilt 7615 56 Male 8 Current 40 Cancer Squamous NA 0.520
MZEB34826E12101XMR1 1 7
Vanderbilt 7753 53 Male 12 Past 22.5 Benign Granuloma NA 0.264
MZEB18626E12101XMR1 1 9
Vanderbilt 4350 78 Female 15 Never 0 Cancer Large Cell NA 0.896
Submitted Manuscript: Confidential
93
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZEB24126E12101XMR1 1 10
Vanderbilt 6519 44 Female 15 Never 0 Benign Granuloma NA 0.338
MZEB19526E12101XMR1 1 11
Vanderbilt 5058 42 Female 17 Past 5 Cancer Other NSCLC Not Specified 0.909
MXCC05426E12101XMR2 1 12 HPS HPS NA NA NA NA NA NA NA NA 0.105 MZEB23526E12101XMR1 1 14
Vanderbilt 6404 73 Male 20 Past 70 Cancer Adenocarcinoma NA 0.866
MZEB32626E12101XMR1 1 15
Vanderbilt 7418 71 Male 12 Never 0 Benign Granuloma NA 0.267
MZEB26626E12101XMR1 1 16
Vanderbilt 6911 67 Male 10 Past 100 Cancer Adenocarcinoma NA 0.799
MZEB35426E12101XMR1 1 17
Vanderbilt 7806 63 Male 10 Current 200 Benign Other Bronchial Epithelial Cells 0.752
MZEB33526E12101XMR1 1 18
Vanderbilt 7658 64 Female 15 Past 40 Benign Granuloma NA 0.767
MZEB35526E12101XMR1 1 19
Vanderbilt 7815 62 Female 11 Past 12 Cancer Adenocarcinoma NA 0.755
MZEB28426E12101XMR1 1 20
Vanderbilt 7072 68 Male 15 Past 50 Benign Other Normal 0.510
MZEB27326E12101XMR1 1 21
Vanderbilt 6969 67 Male 14 Past 40 Cancer Adenocarcinoma NA 0.808
MZEB19026E12101XMR1 1 22
Vanderbilt 4464 63 Female 10 Past 50 Cancer Adenocarcinoma NA 0.688
MZEB34026E12101XMR1 1 23
Vanderbilt 7680 57 Female 10 Current 30 Benign Other
Bronchiolitis Interstitial Fibrosis 0.437
MXCC05426E12101XMR4 1 24 HPS HPS NA NA NA NA NA NA NA NA 0.150 MXCC05426E12101XMR5 2 1 HPS HPS NA NA NA NA NA NA NA NA 0.032
Submitted Manuscript: Confidential
94
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZEB34126E12101XMR1 2 2
Vanderbilt 7696 64 Male 12 Past 52 Benign Other Bronchial Epithelial Cells 0.375
MZEB23626E12101XMR1 2 3
Vanderbilt 6427 84 Female 14 Past 45 Cancer Large Cell NA 0.610
MZEB28126E12101XMR1 2 4
Vanderbilt 7041 49 Male 20 Past 20 Benign Other Bronchial Epithelial Cells 0.293
MZEB19626E12101XMR1 2 5
Vanderbilt 5080 59 Male 20 Past 70.5 Cancer Other NSCLC Not Specified 0.602
MZEB27726E12101XMR1 2 6
Vanderbilt 7020 68 Female 10 Past 3 Cancer Adenocarcinoma NA 0.734
MZEB27526E12101XMR1 2 7
Vanderbilt 6999 35 Female 14 Never 0 Benign Granuloma NA 0.706
MZEB26326E12101XMR1 2 8
Vanderbilt 6897 38 Male 11 Never 0 Benign Other Inflammation 0.572
MZEB30326E12101XMR1 2 9
Vanderbilt 7198 83 Male 19 Past 4 Cancer Adenocarcinoma NA 0.438
MZEB35126E12101XMR1 2 10
Vanderbilt 7785 84 Male 8 Past 40 Cancer Squamous NA 0.892
MZEB35026E12101XMR1 2 11
Vanderbilt 7784 63 Male 11 Never 0 Benign Granuloma NA 0.509
MXCC05426E12101XMR6 2 12 HPS HPS NA NA NA NA NA NA NA NA 0.098 MZEB25426E12101XMR1 2 14
Vanderbilt 6830 36 Male 20 Never 0 Benign Other Emphysematous Lung 0.669
MZEB21826E12101XMR1 2 15
Vanderbilt 5193 39 Male 12 Never 0 Cancer Other Carcinoid 0.770
MZEB19426E12101XMR1 2 16
Vanderbilt 4939 70 Female 8 Past 45 Cancer Adenocarcinoma NA 1.000
MZEB32726E12101XMR1 2 17
Vanderbilt 7450 60 Male 13 Past 50 Benign Granuloma Necrotizing Granuloma 0.719
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95
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MZEB26226E12101XMR1 2 18
Vanderbilt 6885 67 Male 17 Past 90 Benign Other Squamous Metaplasia 0.871
MZEB29126E12101XMR1 2 19
Vanderbilt 7119 76 Male 19 Past 25 Cancer Squamous NA 0.664
MZEB23826E12101XMR1 2 20
Vanderbilt 6440 76 Female 16 Past 5 Cancer Adenocarcinoma NA 0.952
MZEB31626E12101XMR1 2 21
Vanderbilt 7266 61 Female 6 Past 25 Benign Granuloma NA 0.857
MXCC05426E12101XMR8 2 22 HPS HPS NA NA NA NA NA NA NA NA 0.054 MXCC05413F12101XMR1 3 1 HPS HPS NA NA NA NA NA NA NA NA 0.060 MZEB58013F12101XMR1 3 2 IUCPQ 3550 60 Female 14 Past NA Cancer Adenocarcinoma NA 0.832 MZEB53813F12101XMR1 3 3 IUCPQ 4353 60 Female 11 Never 0 Benign Granuloma NA 0.400 MZEB57613F12101XMR1 3 4 IUCPQ 3516 61 Female 12 Past 9.5 Cancer Adenocarcinoma NA 0.906 MZEB57813F12101XMR1 3 5 IUCPQ 3529 56 Female 11 Current 40 Benign Other Pulmonary Infarct 0.115 MZEB59413F12101XMR1 3 6 IUCPQ 3754 69 Male 14.2 Past 30 Benign Other Amyloidosis 0.722 MZEB58813F12101XMR1 3 7 IUCPQ 3735 67 Male 19 Past 50 Cancer Adenocarcinoma NA 0.816 MZEB56613F12101XMR1 3 8 IUCPQ 3463 62 Female 22 Current 39 Cancer Adenocarcinoma NA 0.761 MZEB58413F12101XMR1 3 9 IUCPQ 3664 59 Female 24 Past 47.5 Benign Granuloma NA 0.586 MZEB55513F12101XMR1 3 10 IUCPQ 3363 58 Female 17 Current 13.8 Cancer Adenocarcinoma NA 0.158
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96
Table S9. Experimental design of the validation study.
Sam
ple
nam
e
Bat
ch
Pos
itio
n
Site
Subj
ect
Age
Gen
der
Nod
ule
size
(m
m)
Smok
ing
stat
us
Smok
ing
pack
-yea
rs
Dis
ease
st
atus
His
tolo
gy
subg
roup
His
tolo
gy
spec
ific
Cla
ssif
ier
scor
e
MXCC05413F12101XMR2 3 12 HPS HPS NA NA NA NA NA NA NA NA 0.111 MZEB53713F12101XMR1 3 14 IUCPQ 4229 60 Male 12 Past 40 Benign Hamartoma NA 0.943 MZEB59513F12101XMR1 3 15 IUCPQ 3755 58 Male 14 Past 40 Cancer Adenocarcinoma NA 0.793 MZEB54013F12101XMR1 3 16 IUCPQ 4454 68 Female 11 Never 0 Benign Granuloma NA 0.988 MZEB60113F12101XMR1 3 17 IUCPQ 3823 67 Female 13 Past 35 Cancer Squamous NA 0.994 MXCC05413F12101XMR6 3 24 HPS HPS NA NA NA NA NA NA NA NA 0.677
Note:
• Sample name: Sample identifier
• Batch: Experimental batch
• Position: Sample position in the batch
• Site
o Participating study sites: IUCPQ (Institut Universitaire de Cardiologie et de Pneumologie de Quebec), NYU (New
York University), UPenn (University of Pennsylvania), and Vanderbilt (Vanderbilt University). HPS (human
plasma standard) samples are also listed.
• Subject: Unique subject identifier by study site.
• Age: Age of patient
• Gender: Female/Male
• Nodule size (mm): Radiological nodule size.
• Smoking status: Never/Former/Current
Submitted Manuscript: Confidential
97
• Smoking pack-years: Smoking history pack-years.
• Disease status: Benign/Cancer
• Histology subgroup
o Benign – Granuloma, Hamartoma, Scar, Other.
o Cancer – Adenocarcinoma, Squamous, Large Cell, BAC, Mixed, Other.
• Histology specific: Specific histology
• Classifier score: Score by the 13-protein lung nodule classifier.
Submitted Manuscript: Confidential
98
Table S10. Impact of clinical characteristics on classifier score.
Continuous clinical characteristics Characteristics Sample
Group Pearson Correlation
Coefficient of Linear Fit
95% CI* of Coefficient
p-value on Coefficient
Subject Age All 0.190 0.005 (0.002, -0.008) 0.003 Cancer 0.015 0.000 (-0.004, -0.004) 0.871 Benign 0.227 0.005 (0.001, -0.010) 0.012 Smoking history pack-years All 0.185 0.002 (0.000, -0.003) 0.005 Cancer 0.089 0.001 (-0.001, -0.002) 0.339 Benign 0.139 0.001 (0.000, -0.003) 0.140 Nodule Size All -0.071 -0.003 (-0.008, -0.002) 0.267 Cancer -0.081 -0.003 (-0.009, -0.003) 0.368 Benign -0.035 -0.001 (-0.008, -0.005) 0.700 Categorical clinical characteristics Characteristics Classifier
Score Cancer p-value on
Cancer Benign p-value on
Benign Gender 0.477† 0.110†
Female Median (quartile range)
0.786 (0.602-0.894)
0.479 (0.282-0.721)
Male Median (quartile range)
0.815 (0.705-0.885)
0.570 (0.329-0.801)
Smoking history status
0.652‡ 0.539‡
Never Median (quartile range)
0.707 (0.558-0.841)
0.468 (0.317-0.706)
Past Median (quartile range)
0.804 (0.616-0.892)
0.510 (0.289-0.774)
Current Median (quartile range)
0.790 (0.597-0.876)
0.672 (0.437-0.759)
*Confidence interval (CI). †p-value by Mann-Whitney test. ‡ p-value by Kruskal-Wallis test.
Submitted Manuscript: Confidential
99
Table S11. List of endogenous normalizing proteins.
Normalizing protein Transition
Median technical CV (%)
Median column drift (%)
PEDF_HUMAN LQSLFDSPDFSK_692.34_593.30 25.8 6.8 MASP1_HUMAN TGVITSPDFPNPYPK_816.92_258.10 26.5 18.3 GELS_HUMAN TASDFITK_441.73_710.40 27.1 16.8 LUM_HUMAN SLEDLQLTHNK_433.23_499.30 27.1 16.1 C163A_HUMAN INPASLDK_429.24_630.30 26.6 14.6 PTPRJ_HUMAN VITEPIPVSDLR_669.89_896.50 27.2 18.2 Normalization by panel of transitions 25.1 9.0 Without normalization 32.3 23.8
Shown are the six endogenous normalizing proteins, the corresponding transitions, and the median technical coefficients of variation (CVs) and the median column drifts before and after normalization by individual transitions and by panel of all six transitions. See also Fig. S5.
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100
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
1433E EDLVYQAK 16 4 12 0 NA NA NA 16 4 12 0 NA NA NA 1433E IISSIEQK 16 4 12 0 NA NA NA 0 0 0 0 ND ND ND 1433T AVTEQGAELSNEER 127 57 60 10 NA NA NA 0 0 0 0 ND ND ND 1433T TAFDEAIAELDTLNEDSYK 127 57 60 10 NA NA NA 127 57 60 10 0.623 4.02E-02 7.78E-03 1433Z FLIPNASQAESK 157 72 71 14 NA NA NA 157 72 71 14 0.993 5.49E-05 8.51E-05 1433Z SVTEQGAELSNEER 157 72 71 14 NA NA NA 0 0 0 0 ND ND ND 6PGD AGQAVDDFIEK 90 37 46 7 NA NA NA 0 0 0 0 ND ND ND 6PGD LVPLLDTGDIIIDGGNSEYR 90 37 46 7 NA NA NA 90 37 46 7 0.668 3.21E-02 6.59E-03 A1AG1 WFYIASAFR 157 72 70 15 NA NA NA 0 0 0 0 ND ND ND A1AG1 YVGGQEHFAHLLILR 157 72 70 15 NA NA NA 157 72 70 15 0.980 4.76E-04 3.18E-04 ABCD1 DAGIALLSITHRPSLWK 9 4 5 0 NA NA NA 0 0 0 0 ND ND ND ABCD1 GLQAPAGEPTQEASGVAA
AK 9 4 5 0 NA NA NA 0 0 0 0 ND ND ND
ABCD1 NLLTAAADAIER 9 4 5 0 NA NA NA 9 4 5 0 NA NA NA ADML LAHQIYQFTDK 27 12 15 0 NA NA NA 27 12 15 0 NA NA NA ADML SPEDSSPDAAR 27 12 15 0 NA NA NA 0 0 0 0 ND ND ND AIFM1 ELWFSDDPNVTK 158 72 71 15 NA NA NA 158 72 71 15 0.295 2.30E-01 3.64E-02 AIFM1 GVIFYLR 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND ALDOA ADDGRPFPQVIK 158 72 71 15 0.935 2.17E-03 2.48E-03 141 66 67 8 0.827 1.09E-02 2.82E-03 ALDOA ALQASALK 158 72 71 15 0.935 2.17E-03 2.48E-03 17 6 4 7 0.989 1.92E-04 1.89E-04 AMPN ALEQALEK 158 72 71 15 0.837 9.64E-03 7.21E-03 158 72 71 15 0.804 1.36E-02 3.33E-03 AMPN DHSAIPVINR 158 72 71 15 0.837 9.64E-03 7.21E-03 0 0 0 0 0.886 4.83E-03 1.47E-03 APOA1 AKPALEDLR 158 72 71 15 0.976 6.77E-04 1.78E-03 158 72 71 15 0.998 9.15E-06 2.99E-05 APOA1 ATEHLSTLSEK 158 72 71 15 0.976 6.77E-04 1.78E-03 0 0 0 0 0.998 9.15E-06 2.99E-05 APOE AATVGSLAGQPLQER 158 72 71 15 0.966 9.61E-04 1.78E-03 158 72 71 15 0.989 1.74E-04 1.89E-04 APOE LGPLVEQGR 158 72 71 15 0.966 9.61E-04 1.78E-03 0 0 0 0 0.989 1.92E-04 1.89E-04 BGH3 LTLLAPLNSVFK 158 72 71 15 0.804 1.36E-02 9.86E-03 0 0 0 0 0.976 7.05E-04 3.82E-04
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101
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
BGH3 SPYQLVLQHSR 158 72 71 15 0.804 1.36E-02 9.86E-03 158 72 71 15 0.872 6.03E-03 1.74E-03 BST1 GEGTSAHLR 157 71 71 15 NA NA NA 0 0 0 0 ND ND ND BST1 GFFADYEIPNLQK 157 71 71 15 NA NA NA 157 71 71 15 0.903 3.72E-03 1.20E-03 C163A INPASLDK 158 72 71 15 0.694 2.81E-02 1.38E-02 11 4 5 2 0.905 3.60E-03 1.19E-03 C163A LEVFYNGAWGTVGK 158 72 71 15 0.694 2.81E-02 1.38E-02 49 27 21 1 NA NA NA C163A TSYQVYSK 158 72 71 15 0.694 2.81E-02 1.38E-02 98 41 45 12 0.710 2.57E-02 5.65E-03 CALU EQFVEFR 120 59 55 6 NA NA NA 120 59 55 6 0.910 3.25E-03 1.11E-03 CALU TFDQLTPEESK 120 59 55 6 NA NA NA 0 0 0 0 ND ND ND CATB LPASFDAR 62 34 28 0 NA NA NA 62 34 28 0 0.581 4.92E-02 9.05E-03 CATB TDQYWEK 62 34 28 0 NA NA NA 0 0 0 0 ND ND ND CATG NVNPVALPR 14 4 9 1 NA NA NA 0 0 0 0 ND ND ND CATG SSGVPPEVFTR 14 4 9 1 NA NA NA 14 4 9 1 0.934 2.19E-03 8.47E-04 CBPB2 DTGTYGFLLPER 158 72 71 15 NA NA NA 158 72 71 15 0.982 3.94E-04 2.97E-04 CBPB2 EAFAAVSK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND CD14 ATVNPSAPR 158 72 71 15 0.714 2.52E-02 1.37E-02 0 0 0 0 0.932 2.28E-03 8.71E-04 CD14 SWLAELQQWLKPGLK 158 72 71 15 0.714 2.52E-02 1.37E-02 158 72 71 15 0.993 5.49E-05 8.51E-05 CD44 FAGVFHVEK 158 72 71 15 0.898 4.09E-03 3.81E-03 158 72 71 15 0.814 1.23E-02 3.10E-03 CD44 YGFIEGHVVIPR 158 72 71 15 0.898 4.09E-03 3.81E-03 0 0 0 0 0.982 4.39E-04 3.15E-04 CD59 AGLQVYNK 156 71 71 14 NA NA NA 156 71 71 14 0.867 6.49E-03 1.85E-03 CD59 TVLLLVTPFLAAAWSLHP 156 71 71 14 NA NA NA 0 0 0 0 ND ND ND CDCP1 EEGVFTVTPDTK 157 71 71 15 NA NA NA 0 0 0 0 ND ND ND CDCP1 LSLVLVPAQK 157 71 71 15 NA NA NA 157 71 71 15 0.980 4.76E-04 3.18E-04 CEAM8 LFIPNITTK 79 36 41 2 NA NA NA 79 36 41 2 NA NA NA CEAM8 TLTLLSVTR 79 36 41 2 NA NA NA 0 0 0 0 ND ND ND CERU GAYPLSIEPIGVR 158 72 71 15 0.184 3.97E-01 1.35E-01 0 0 0 0 0.876 5.57E-03 1.64E-03 CERU GPEEEHLGILGPVIWAEVG
DTIR 158 72 71 15 0.184 3.97E-01 1.35E-01 158 72 71 15 0.337 1.83E-01 2.92E-02
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102
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
CERU NNEGTYYSPNYNPQSR 158 72 71 15 0.184 3.97E-01 1.35E-01 0 0 0 0 ND ND ND CH10 GGEIQPVSVK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND CH10 VLLPEYGGTK 158 72 71 15 NA NA NA 158 72 71 15 -
0.288 9.54E-01 1.40E-01
CLIC1 FSAYIK 137 70 65 2 0.965 1.05E-03 1.78E-03 8 4 4 0 0.987 2.47E-04 2.20E-04 CLIC1 LAALNPESNTAGLDIFAK 137 70 65 2 0.965 1.05E-03 1.78E-03 129 66 61 2 0.989 1.92E-04 1.89E-04 CLIC1 NSNPALNDNLEK 137 70 65 2 0.965 1.05E-03 1.78E-03 0 0 0 0 NA NA NA CLUS ASSIIDELFQDR 158 72 71 15 0.662 3.32E-02 1.52E-02 0 0 0 0 0.935 2.16E-03 8.47E-04 CLUS EIQNAVNGVK 158 72 71 15 0.662 3.32E-02 1.52E-02 158 72 71 15 0.975 7.14E-04 3.82E-04 CNTN1 AHSDGGDGVVSQVK 158 72 71 15 0.482 8.00E-02 3.11E-02 157 72 70 15 0.679 3.03E-02 6.33E-03 CNTN1 DGEYVVEVR 158 72 71 15 0.482 8.00E-02 3.11E-02 1 0 1 0 0.482 8.01E-02 1.39E-02 CO6A3 IGDLHPQIVNLLK 158 72 71 15 0.743 2.13E-02 1.29E-02 0 0 0 0 0.598 4.55E-02 8.47E-03 CO6A3 VAVVQYSDR 158 72 71 15 0.743 2.13E-02 1.29E-02 158 72 71 15 0.823 1.12E-02 2.85E-03 CO6A3 WYYDPNTK 158 72 71 15 0.743 2.13E-02 1.29E-02 0 0 0 0 ND ND ND COF1 EILVGDVGQTVDDPYATF
VK 127 65 60 2 NA NA NA 0 0 0 0 ND ND ND
COF1 LGGSAVISLEGKPL 127 65 60 2 NA NA NA 0 0 0 0 ND ND ND COF1 YALYDATYETK 127 65 60 2 NA NA NA 127 65 60 2 0.963 1.11E-03 5.09E-04 COIA1 AVGLAGTFR 158 72 71 15 0.616 4.18E-02 1.80E-02 37 16 13 8 0.909 3.35E-03 1.12E-03 COIA1 TEAPSATGQASSLLGGR 158 72 71 15 0.616 4.18E-02 1.80E-02 121 56 58 7 0.440 1.01E-01 1.69E-02 CRP APLTKPLK 153 70 68 15 0.991 1.19E-04 1.09E-03 21 13 7 1 0.994 5.49E-05 8.51E-05 CRP ESDTSYVSLK 153 70 68 15 0.991 1.19E-04 1.09E-03 132 57 61 14 0.999 9.15E-06 2.99E-05 CRP YEVQGEVFTKPQLWP 153 70 68 15 0.991 1.19E-04 1.09E-03 0 0 0 0 ND ND ND CSF1 FNSVPLTDTGHER 134 64 59 11 -
0.117 8.66E-01 2.62E-01 113 56 50 7 0.631 3.86E-02 7.66E-03
CSF1 ISSLRPQGLSNPSTLSAQPQLSR
134 64 59 11 -0.117
8.66E-01 2.62E-01 21 8 9 4 NA NA NA
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103
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
CYTB SQLEEK 100 50 48 2 NA NA NA 0 0 0 0 ND ND ND CYTB SQVVAGTNYFIK 100 50 48 2 NA NA NA 100 50 48 2 0.924 2.59E-03 9.41E-04 DESP YGDGIQLTR 131 59 60 12 NA NA NA 131 59 60 12 NA NA NA DMKN QVPGFGVADALGNR 128 57 56 15 NA NA NA 0 0 0 0 ND ND ND DMKN VSEALGQGTR 128 57 56 15 NA NA NA 128 57 56 15 0.608 4.32E-02 8.21E-03 DSG2 GQIIGNFQAFDEDTGLPAH
AR 158 72 71 15 0.096 5.55E-01 1.78E-01 1 0 0 1 0.628 3.92E-02 7.68E-03
DSG2 ILDVNDNIPVVENK 158 72 71 15 0.096 5.55E-01 1.78E-01 157 72 71 14 0.039 6.57E-01 9.82E-02 EF1A1 IGGIGTVPVGR 158 72 71 15 -
0.004 7.28E-01 2.31E-01 158 72 71 15 0.930 2.35E-03 8.80E-04
EF1A1 QTVAVGVIK 158 72 71 15 -0.004
7.28E-01 2.31E-01 0 0 0 0 0.309 2.15E-01 3.41E-02
EF2 FSVSPVVR 125 61 55 9 NA NA NA 125 61 55 9 0.573 5.14E-02 9.33E-03 EF2 GVQYLNEIK 125 61 55 9 NA NA NA 0 0 0 0 ND ND ND ENOA AVEHINK 156 72 70 14 NA NA NA 0 0 0 0 ND ND ND ENOA YISPDQLADLYK 156 72 70 14 NA NA NA 156 72 70 14 0.802 1.37E-02 3.33E-03 ENOA YNQLLR 156 72 70 14 NA NA NA 0 0 0 0 ND ND ND ENPL SGTSEFLNK 158 72 71 15 0.735 2.23E-02 1.29E-02 1 0 1 0 0.704 2.67E-02 5.74E-03 ENPL SGYLLPDTK 158 72 71 15 0.735 2.23E-02 1.29E-02 157 72 70 15 0.904 3.64E-03 1.19E-03 EPHB6 RPHFDQLVAAFDK 157 72 70 15 NA NA NA 0 0 0 0 ND ND ND EPHB6 WAAPEVIAHGK 157 72 70 15 NA NA NA 157 72 70 15 -
0.078 8.29E-01 1.23E-01
ERBB3 GESIEPLDPSEK 105 44 49 12 NA NA NA 0 0 0 0 ND ND ND ERBB3 LAEVPDLLEK 105 44 49 12 NA NA NA 105 44 49 12 0.042 6.52E-01 9.79E-02 EREG VAQVSITK 115 58 56 1 NA NA NA 115 58 56 1 0.531 6.24E-02 1.10E-02 EREG VTSGDPELPQV 115 58 56 1 NA NA NA 0 0 0 0 ND ND ND ERO1A AVLQWTK 121 57 52 12 NA NA NA 0 0 0 0 ND ND ND
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Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
ERO1A LLESDYFR 121 57 52 12 NA NA NA 0 0 0 0 ND ND ND ERO1A NLLQNIH 121 57 52 12 NA NA NA 0 0 0 0 ND ND ND ERO1A VLPFFERPDFQLFTGNK 121 57 52 12 NA NA NA 121 57 52 12 0.467 8.69E-02 1.48E-02 F10A1 AIDLFTDAIK 35 15 20 0 NA NA NA 0 0 0 0 ND ND ND F10A1 LQKPNAAIR 35 15 20 0 NA NA NA 35 15 20 0 NA NA NA FAM3C GINVALANGK 97 51 37 9 0.554 5.63E-02 2.32E-02 88 46 34 8 0.618 4.13E-02 7.95E-03 FAM3C SALDTAAR 97 51 37 9 0.554 5.63E-02 2.32E-02 9 5 3 1 -
0.769 9.99E-01 1.45E-01
FAM3C TGEVLDTK 97 51 37 9 0.554 5.63E-02 2.32E-02 0 0 0 0 ND ND ND FCGR1 HLEEELK 39 15 22 2 NA NA NA 0 0 0 0 ND ND ND FCGR1 VFTEGEPLALR 39 15 22 2 NA NA NA 39 15 22 2 NA NA NA FIBA GGSTSYGTGSETESPR 147 67 65 15 0.965 1.02E-03 1.78E-03 108 47 46 15 0.998 9.15E-06 2.99E-05 FIBA NSLFEYQK 147 67 65 15 0.965 1.02E-03 1.78E-03 39 20 19 0 0.999 9.15E-06 2.99E-05 FINC SYTITGLQPGTDYK 154 70 69 15 0.600 4.50E-02 1.90E-02 135 61 59 15 0.982 4.39E-04 3.15E-04 FINC VPGTSTSATLTGLTR 154 70 69 15 0.600 4.50E-02 1.90E-02 19 9 10 0 0.695 2.79E-02 5.86E-03 FKB11 ANYWLK 23 8 12 3 NA NA NA 0 0 0 0 ND ND ND FKB11 DPLVIELGQK 23 8 12 3 NA NA NA 23 8 12 3 NA NA NA FOLH1 GVILYSDPADYFAPGVK 138 62 62 14 NA NA NA 0 0 0 0 ND ND ND FOLH1 LGSGNDFEVFFQR 138 62 62 14 NA NA NA 138 62 62 14 0.706 2.65E-02 5.74E-03 FRIL DDVALEGVSHFFR 151 71 70 10 NA NA NA 0 0 0 0 ND ND ND FRIL LGGPEAGLGEYLFER 151 71 70 10 NA NA NA 151 71 70 10 0.980 5.13E-04 3.35E-04 G3P GALQNIIPASTGAAK 150 72 70 8 0.936 2.11E-03 2.48E-03 149 72 69 8 0.965 1.05E-03 4.92E-04 G3P LISWYDNEFGYSNR 150 72 70 8 0.936 2.11E-03 2.48E-03 1 0 1 0 0.958 1.29E-03 5.75E-04 G6PD DGLLPENTFIVGYAR 43 19 24 0 NA NA NA 43 19 24 0 0.995 4.58E-05 8.51E-05 G6PD GGYFDEFGIIR 43 19 24 0 NA NA NA 0 0 0 0 ND ND ND G6PI AVLHVALR 39 15 22 2 0.951 1.60E-03 2.10E-03 6 4 2 0 0.758 1.95E-02 4.47E-03 G6PI TLAQLNPESSLFIIASK 39 15 22 2 0.951 1.60E-03 2.10E-03 33 11 20 2 0.865 6.77E-03 1.91E-03
Submitted Manuscript: Confidential
105
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
GDIR2 DIVSGLK 158 72 71 15 0.151 4.54E-01 1.50E-01 158 72 71 15 0.753 2.01E-02 4.58E-03 GDIR2 LNYKPPPQK 158 72 71 15 0.151 4.54E-01 1.50E-01 0 0 0 0 0.929 2.36E-03 8.80E-04 GELS AQPVQVAEGSEPDGFWEA
LGGK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND
GELS TASDFITK 158 72 71 15 NA NA NA 158 72 71 15 0.981 4.67E-04 3.18E-04 GGH NLDGISHAPNAVK 158 72 71 15 0.772 1.75E-02 1.19E-02 158 72 71 15 0.795 1.48E-02 3.48E-03 GGH YYIAASYVK 158 72 71 15 0.772 1.75E-02 1.19E-02 0 0 0 0 0.845 8.66E-03 2.34E-03 GRP78 TWNDPSVQQDIK 158 72 71 15 0.477 8.22E-02 3.13E-02 90 42 44 4 0.843 8.91E-03 2.38E-03 GRP78 VYEGERPLTK 158 72 71 15 0.477 8.22E-02 3.13E-02 68 30 27 11 0.260 2.78E-01 4.35E-02 GSLG1 IIIQESALDYR 158 72 71 15 NA NA NA 158 72 71 15 0.574 5.11E-02 9.33E-03 GSLG1 LDPALQDK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND GSLG1 LIAQDYK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND GSLG1 NDINILK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND GSTP1 ALPGQLKPFETLLSQNQG
GK 123 61 61 1 NA NA NA 123 61 61 1 0.973 7.87E-04 4.13E-04
GSTP1 YISLIYTNYEAGK 123 61 61 1 NA NA NA 0 0 0 0 ND ND ND HPSE LPYPFSNK 49 22 24 3 NA NA NA 0 0 0 0 ND ND ND HPSE SVQLNGLTLK 49 22 24 3 NA NA NA 49 22 24 3 NA NA NA HPT VGYVSGWGR 158 72 71 15 0.994 5.49E-05 1.09E-03 0 0 0 0 0.997 9.15E-06 2.99E-05 HPT VTSIQDWVQK 158 72 71 15 0.994 5.49E-05 1.09E-03 158 72 71 15 1.000 9.15E-06 2.99E-05 HS90A SLTNDWEDHLAVK 32 16 15 1 NA NA NA 32 16 15 1 -
0.483 9.87E-01 1.44E-01
HS90B ADHGEPIGR 121 58 61 2 NA NA NA 0 0 0 0 ND ND ND HS90B IDIIPNPQER 121 58 61 2 NA NA NA 121 58 61 2 0.945 1.72E-03 7.13E-04 HS90B NPDDITQEEYGEFYK 121 58 61 2 NA NA NA 0 0 0 0 ND ND ND HSPB1 DGVVEITGK 30 14 14 2 NA NA NA 0 0 0 0 ND ND ND HSPB1 GPSWDPFR 30 14 14 2 NA NA NA 30 14 14 2 NA NA NA
Submitted Manuscript: Confidential
106
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
HTRA1 LHRPPVIVLQR 40 13 18 9 NA NA NA 40 13 18 9 0.671 3.16E-02 6.55E-03 HTRA1 LPVLLLGR 40 13 18 9 NA NA NA 0 0 0 0 ND ND ND HTRA1 VTAGISFAIPSDK 40 13 18 9 NA NA NA 0 0 0 0 ND ND ND HXK1 FLLSESGSGK 117 52 55 10 -
0.045 7.88E-01 2.41E-01 17 7 6 4 NA NA NA
HXK1 LVDEYSLNAGK 117 52 55 10 -0.045
7.88E-01 2.41E-01 47 24 21 2 NA NA NA
HXK1 SANLVAATLGAILNR 117 52 55 10 -0.045
7.88E-01 2.41E-01 53 21 28 4 NA NA NA
HYOU1 FPEHELTFDPQR 156 72 71 13 0.326 1.95E-01 7.05E-02 0 0 0 0 0.468 8.62E-02 1.47E-02 HYOU1 LPATEKPVLLSK 156 72 71 13 0.326 1.95E-01 7.05E-02 156 72 71 13 0.545 5.86E-02 1.04E-02 IBP2 AEVLFR 158 72 71 15 0.948 1.66E-03 2.10E-03 0 0 0 0 0.881 5.25E-03 1.58E-03 IBP2 ELAVFR 158 72 71 15 0.948 1.66E-03 2.10E-03 158 72 71 15 0.985 2.84E-04 2.39E-04 IBP2 LIQGAPTIR 158 72 71 15 0.948 1.66E-03 2.10E-03 0 0 0 0 0.970 8.70E-04 4.26E-04 IBP3 FHPLHSK 158 72 71 15 0.915 3.01E-03 2.92E-03 0 0 0 0 0.976 7.14E-04 3.82E-04 IBP3 FLNVLSPR 158 72 71 15 0.915 3.01E-03 2.92E-03 0 0 0 0 0.993 5.49E-05 8.51E-05 IBP3 YGQPLPGYTTK 158 72 71 15 0.915 3.01E-03 2.92E-03 158 72 71 15 0.448 9.70E-02 1.63E-02 ICAM1 ASVSVTAEDEGTQR 114 50 57 7 NA NA NA 0 0 0 0 ND ND ND ICAM1 VELAPLPSWQPVGK 114 50 57 7 NA NA NA 114 50 57 7 0.293 2.34E-01 3.68E-02 ICAM3 IALETSLSK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND ICAM3 TFVLPVTPPR 158 72 71 15 NA NA NA 158 72 71 15 0.923 2.67E-03 9.59E-04 IF4A1 GYDVIAQAQSGTGK 58 26 32 0 NA NA NA 0 0 0 0 ND ND ND IF4A1 VLITTDLLAR 58 26 32 0 NA NA NA 58 26 32 0 NA NA NA IGF1 EGTEASLQIR 40 24 16 0 NA NA NA 0 0 0 0 ND ND ND IGF1 ISSLPTQLFK 40 24 16 0 NA NA NA 40 24 16 0 NA NA NA IL18 SDIIFFQR 45 21 24 0 NA NA NA 45 21 24 0 0.594 4.63E-02 8.57E-03 IL18 SVPGHDNK 45 21 24 0 NA NA NA 0 0 0 0 ND ND ND
Submitted Manuscript: Confidential
107
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
ILEU EATTNAPFR 88 44 44 0 0.989 1.92E-04 1.25E-03 13 5 8 0 0.993 6.41E-05 8.98E-05 ILEU TYNFLPEFLVSTQK 88 44 44 0 0.989 1.92E-04 1.25E-03 75 39 36 0 0.995 4.58E-05 8.51E-05 ILK HSGIDFK 90 40 45 5 0.887 4.78E-03 4.04E-03 15 9 6 0 0.803 1.36E-02 3.33E-03 ILK QLNFLTK 90 40 45 5 0.887 4.78E-03 4.04E-03 75 31 39 5 0.917 2.97E-03 1.04E-03 ILK WQGNDIVVK 90 40 45 5 0.887 4.78E-03 4.04E-03 0 0 0 0 ND ND ND INHBA AEVWLFLK 32 16 14 2 NA NA NA 0 0 0 0 ND ND ND INHBA EGSDLSVVER 32 16 14 2 NA NA NA 32 16 14 2 -
0.573 9.93E-01 1.45E-01
ISLR ALPGTPVASSQPR 158 72 71 15 0.736 2.22E-02 1.29E-02 0 0 0 0 0.724 2.37E-02 5.24E-03 ISLR EVPLLQSLWLAHNEIR 158 72 71 15 0.736 2.22E-02 1.29E-02 0 0 0 0 0.838 9.46E-03 2.51E-03 ISLR LPGLPEGAFR 158 72 71 15 0.736 2.22E-02 1.29E-02 158 72 71 15 0.835 9.84E-03 2.59E-03 ITA5 SLQWFGATVR 114 55 53 6 NA NA NA 114 55 53 6 0.436 1.03E-01 1.72E-02 ITA5 SSASSGPQILK 114 55 53 6 NA NA NA 0 0 0 0 ND ND ND K1C18 LASYLDR 72 37 31 4 NA NA NA 0 0 0 0 ND ND ND K1C18 LQLETEIEALK 72 37 31 4 NA NA NA 72 37 31 4 NA NA NA K1C18 VVSETNDTK 72 37 31 4 NA NA NA 0 0 0 0 ND ND ND K1C19 FGAQLAHIQALISGIEAQL
GDVR 158 72 71 15 NA NA NA 158 72 71 15 0.399 1.28E-01 2.10E-02
K1C19 FGPGVAFR 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND KIT QATLTISSAR 158 72 71 15 0.481 8.03E-02 3.11E-02 158 72 71 15 0.700 2.72E-02 5.76E-03 KIT YVSELHLTR 158 72 71 15 0.481 8.03E-02 3.11E-02 0 0 0 0 0.811 1.26E-02 3.15E-03 KLK14 VLGSGTWPSAPK 27 17 10 0 NA NA NA 27 17 10 0 NA NA NA KLK14 VSGWGTISSPIAR 27 17 10 0 NA NA NA 0 0 0 0 ND ND ND KPYM APIIAVTR 158 72 71 15 0.965 1.04E-03 1.78E-03 13 3 3 7 0.993 6.41E-05 8.98E-05 KPYM LDIDSPPITAR 158 72 71 15 0.965 1.04E-03 1.78E-03 145 69 68 8 0.952 1.58E-03 6.75E-04 LAMB2 IQGTLQPHAR 69 34 35 0 -
0.348 9.68E-01 2.83E-01 0 0 0 0 ND ND ND
Submitted Manuscript: Confidential
108
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
LAMB2 SLADVDAILAR 69 34 35 0 -0.348
9.68E-01 2.83E-01 31 14 17 0 NA NA NA
LAMB2 VLELSIPASAEQIQHLAGAIAER
69 34 35 0 -0.348
9.68E-01 2.83E-01 38 20 18 0 NA NA NA
LDHA FIIPNVVK 157 72 71 14 0.890 4.58E-03 4.04E-03 0 0 0 0 0.942 1.82E-03 7.34E-04 LDHA LVIITAGAR 157 72 71 14 0.890 4.58E-03 4.04E-03 157 72 71 14 0.943 1.81E-03 7.34E-04 LDHB FIIPQIVK 158 72 71 15 0.759 1.93E-02 1.28E-02 157 72 71 14 0.954 1.53E-03 6.61E-04 LDHB GLTSVINQK 158 72 71 15 0.759 1.93E-02 1.28E-02 1 0 0 1 0.889 4.68E-03 1.45E-03 LEG1 GEVAPDAK 146 68 70 8 NA NA NA 0 0 0 0 ND ND ND LEG1 LPDGYEFK 146 68 70 8 NA NA NA 0 0 0 0 ND ND ND LEG1 SFVLNLGK 146 68 70 8 NA NA NA 146 68 70 8 0.702 2.69E-02 5.74E-03 LG3BP ASHEEVEGLVEK 158 72 71 15 0.962 1.16E-03 1.78E-03 158 72 71 15 0.984 3.84E-04 2.97E-04 LG3BP VEIFYR 158 72 71 15 0.962 1.16E-03 1.78E-03 0 0 0 0 0.990 1.19E-04 1.40E-04 LG3BP YSSDYFQAPSDYR 158 72 71 15 0.962 1.16E-03 1.78E-03 0 0 0 0 0.986 2.47E-04 2.20E-04 LRP1 TVLWPNGLSLDIPAGR 158 72 71 15 -
0.282 9.53E-01 2.83E-01 158 72 71 15 0.976 6.96E-04 3.82E-04
LRP1 VFFTDYGQIPK 158 72 71 15 -0.282
9.53E-01 2.83E-01 0 0 0 0 0.064 6.13E-01 9.25E-02
LUM NIPTVNENLENYYLEVNQLEK
158 72 71 15 0.917 2.95E-03 2.92E-03 158 72 71 15 0.978 5.77E-04 3.53E-04
LUM SLEDLQLTHNK 158 72 71 15 0.917 2.95E-03 2.92E-03 0 0 0 0 0.976 7.14E-04 3.82E-04 LYOX HWFQAGYSTSR 121 54 53 14 NA NA NA 0 0 0 0 ND ND ND LYOX TPILLIR 121 54 53 14 NA NA NA 121 54 53 14 0.599 4.53E-02 8.47E-03 MASP1 APGELEHGLITFSTR 158 72 71 15 0.457 9.16E-02 3.43E-02 151 68 70 13 0.796 1.46E-02 3.47E-03 MASP1 TGVITSPDFPNPYPK 158 72 71 15 0.457 9.16E-02 3.43E-02 7 4 1 2 0.958 1.31E-03 5.75E-04 MDHC LGVTANDVK 130 63 62 5 NA NA NA 130 63 62 5 0.547 5.79E-02 1.03E-02 MDHC VLVTGAAGQIAYSLLYSIG 130 63 62 5 NA NA NA 0 0 0 0 ND ND ND
Submitted Manuscript: Confidential
109
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
NGSVFGK MDHM VDFPQDQLTALTGR 158 72 71 15 NA NA NA 158 72 71 15 0.557 5.54E-02 1.00E-02 MDHM VSSFEEK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND MMP12 FLLILLLQATASGALPLNSS
TSLEK 158 72 71 15 NA NA NA 158 72 71 15 0.822 1.13E-02 2.87E-03
MMP12 GIQSLYGDPK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND MMP12 IDAVFYSK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND MMP2 AFQVWSDVTPLR 153 72 71 10 0.666 3.24E-02 1.52E-02 152 72 71 9 0.911 3.22E-03 1.11E-03 MMP2 IIGYTPDLDPETVDDAFAR 153 72 71 10 0.666 3.24E-02 1.52E-02 1 0 0 1 0.659 3.36E-02 6.82E-03 MMP7 LSQDDIK 102 49 47 6 NA NA NA 102 49 47 6 0.452 9.46E-02 1.60E-02 MMP7 NANSLEAK 102 49 47 6 NA NA NA 0 0 0 0 ND ND ND MMP9 AFALWSAVTPLTFTR 158 72 71 15 0.850 8.18E-03 6.32E-03 50 15 20 15 0.749 2.06E-02 4.62E-03 MMP9 FQTFEGDLK 158 72 71 15 0.850 8.18E-03 6.32E-03 108 57 51 0 0.826 1.09E-02 2.82E-03 MMP9 SLGPALLLLQK 158 72 71 15 0.850 8.18E-03 6.32E-03 0 0 0 0 0.970 8.88E-04 4.28E-04 MPRI GHQAFDVGQPR 158 72 71 15 0.203 3.64E-01 1.27E-01 23 11 9 3 0.384 1.40E-01 2.28E-02 MPRI TYHSVGDSVLR 158 72 71 15 0.203 3.64E-01 1.27E-01 4 3 0 1 0.375 1.47E-01 2.40E-02 MPRI VPIDGPPIDIGR 158 72 71 15 0.203 3.64E-01 1.27E-01 131 58 62 11 0.350 1.71E-01 2.75E-02 NCF4 AEALFDFTGNSK 138 62 61 15 0.695 2.80E-02 1.38E-02 43 18 21 4 NA NA NA NCF4 DAEGDLVR 138 62 61 15 0.695 2.80E-02 1.38E-02 0 0 0 0 ND ND ND NCF4 DIAVEEDLSSTPLLK 138 62 61 15 0.695 2.80E-02 1.38E-02 0 0 0 0 ND ND ND NCF4 GATGIFPLSFVK 138 62 61 15 0.695 2.80E-02 1.38E-02 95 44 40 11 0.972 8.15E-04 4.13E-04 NDKB DRPFFPGLVK 24 11 13 0 NA NA NA 0 0 0 0 ND ND ND NDKB NIIHGSDSVK 24 11 13 0 NA NA NA 24 11 13 0 0.419 1.14E-01 1.88E-02 NRP1 FVSDYETHGAGFSIR 158 72 71 15 0.718 2.45E-02 1.37E-02 0 0 0 0 0.481 8.03E-02 1.39E-02 NRP1 FVTAVGTQGAISK 158 72 71 15 0.718 2.45E-02 1.37E-02 158 72 71 15 0.660 3.36E-02 6.82E-03 NRP1 SFEGNNNYDTPELR 158 72 71 15 0.718 2.45E-02 1.37E-02 0 0 0 0 0.750 2.05E-02 4.62E-03 OSTP AIPVAQDLNAPSDWDSR 108 51 51 6 NA NA NA 108 51 51 6 0.603 4.44E-02 8.37E-03
Submitted Manuscript: Confidential
110
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
OSTP DSYETSQLDDQSAETHSHK
108 51 51 6 NA NA NA 0 0 0 0 ND ND ND
OSTP YPDAVATWLNPDPSQK 108 51 51 6 NA NA NA 0 0 0 0 ND ND ND PCBP2 IANPVEGSTDR 52 27 23 2 NA NA NA 0 0 0 0 NA NA NA PCBP2 IITLAGPTNAIFK 52 27 23 2 NA NA NA 52 27 23 2 0.169 4.23E-01 6.56E-02 PCYOX IAIIGAGIGGTSAAYYLR 37 19 16 2 NA NA NA 0 0 0 0 ND ND ND PCYOX IFSQETLTK 37 19 16 2 NA NA NA 37 19 16 2 NA NA NA PCYOX TLLETLQK 37 19 16 2 NA NA NA 0 0 0 0 ND ND ND PDGFB SFDDLQR 111 57 51 3 0.212 3.49E-01 1.24E-01 99 48 48 3 0.080 5.83E-01 8.84E-02 PDGFB SHSGGELESLAR 111 57 51 3 0.212 3.49E-01 1.24E-01 12 9 3 0 0.109 5.31E-01 8.14E-02 PDIA3 ELSDFISYLQR 129 62 59 8 NA NA NA 129 62 59 8 0.894 4.27E-03 1.35E-03 PDIA3 SEPIPESNDGPVK 129 62 59 8 NA NA NA 0 0 0 0 ND ND ND PDIA4 FDVSGYPTIK 81 35 42 4 NA NA NA 81 35 42 4 0.481 8.05E-02 1.39E-02 PDIA4 FHHTFSTEIAK 81 35 42 4 NA NA NA 0 0 0 0 ND ND ND PECA1 SELVTVTESFSTPK 77 39 34 4 NA NA NA 0 0 0 0 ND ND ND PECA1 STESYFIPEVR 77 39 34 4 NA NA NA 77 39 34 4 NA NA NA PEDF LQSLFDSPDFSK 158 72 71 15 0.961 1.21E-03 1.78E-03 0 0 0 0 0.990 1.19E-04 1.40E-04 PEDF TVQAVLTVPK 158 72 71 15 0.961 1.21E-03 1.78E-03 158 72 71 15 0.978 5.77E-04 3.53E-04 PGAM1 HGESAWNLENR 14 7 6 1 NA NA NA 14 7 6 1 NA NA NA PLIN2 DAVTTTVTGAK 138 63 61 14 NA NA NA 0 0 0 0 ND ND ND PLIN2 EVSDSLLTSSK 138 63 61 14 NA NA NA 138 63 61 14 0.083 5.79E-01 8.82E-02 PLSL IGNFSTDIK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND PLSL ISFDEFIK 158 72 71 15 NA NA NA 158 72 71 15 0.975 7.14E-04 3.82E-04 PLXB3 ELPVPIYVTQGEAQR 77 40 35 2 NA NA NA 0 0 0 0 ND ND ND PLXB3 GPVDAVTGK 77 40 35 2 NA NA NA 77 40 35 2 NA NA NA PLXC1 FWVNILK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND PLXC1 LNTIGHYEISNGSTIK 158 72 71 15 NA NA NA 158 72 71 15 NA NA NA
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111
Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
POSTN GFEPGVTNILK 158 72 71 15 0.624 3.99E-02 1.75E-02 158 72 71 15 0.935 2.16E-03 8.47E-04 POSTN IIDGVPVEITEK 158 72 71 15 0.624 3.99E-02 1.75E-02 0 0 0 0 0.801 1.40E-02 3.37E-03 POSTN IIHGNQIATNGVVHVIDR 158 72 71 15 0.624 3.99E-02 1.75E-02 0 0 0 0 ND ND ND PPIB VIFGLFGK 158 72 71 15 0.926 2.47E-03 2.69E-03 0 0 0 0 0.863 6.89E-03 1.93E-03 PPIB VYFDLR 158 72 71 15 0.926 2.47E-03 2.69E-03 158 72 71 15 0.888 4.73E-03 1.45E-03 PRDX1 IGHPAPNFK 158 72 71 15 0.860 7.15E-03 5.83E-03 116 57 59 0 0.550 5.74E-02 1.03E-02 PRDX1 QITVNDLPVGR 158 72 71 15 0.860 7.15E-03 5.83E-03 42 15 12 15 0.996 1.83E-05 4.49E-05 PROF1 STGGAPTFNVTVTK 158 72 71 15 0.984 3.57E-04 1.78E-03 157 71 71 15 0.991 9.15E-05 1.22E-04 PROF1 TFVNITPAEVGVLVGK 158 72 71 15 0.984 3.57E-04 1.78E-03 1 1 0 0 0.996 1.83E-05 4.49E-05 PRS6A VDILDPALLR 13 7 5 1 NA NA NA 13 7 5 1 0.986 2.56E-04 2.22E-04 PTGIS DPEIYTDPEVFK 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND PTGIS LLLFPFLSPQR 158 72 71 15 NA NA NA 158 72 71 15 0.159 4.39E-01 6.76E-02 PTPA FGSLLPIHPVTSG 103 55 47 1 NA NA NA 103 55 47 1 0.741 2.15E-02 4.80E-03 PTPA TGPFAEHSNQLWNISAVPS
WSK 103 55 47 1 NA NA NA 0 0 0 0 ND ND ND
PTPA VDDQIAIVFK 103 55 47 1 NA NA NA 0 0 0 0 ND ND ND PTPA WIDETPPVDQPSR 103 55 47 1 NA NA NA 0 0 0 0 ND ND ND PTPRJ AVSISPTNVILTWK 158 72 71 15 0.679 3.04E-02 1.46E-02 0 0 0 0 0.916 2.98E-03 1.04E-03 PTPRJ VITEPIPVSDLR 158 72 71 15 0.679 3.04E-02 1.46E-02 158 72 71 15 0.890 4.60E-03 1.44E-03 PVR SVDIWLR 158 72 71 15 0.659 3.37E-02 1.52E-02 158 72 71 15 0.948 1.66E-03 6.96E-04 PVR VLAKPQNTAEVQK 158 72 71 15 0.659 3.37E-02 1.52E-02 0 0 0 0 0.791 1.52E-02 3.54E-03 RAB32 VHLPNGSPIPAVLLANK 22 1 6 15 NA NA NA 0 0 0 0 ND ND ND RAB32 VLVIGELGVGK 22 1 6 15 NA NA NA 22 1 6 15 NA NA NA RAN FNVWDTAGQEK 116 58 58 0 0.491 7.62E-02 3.05E-02 2 1 1 0 NA NA NA RAN LVLVGDGGTGK 116 58 58 0 0.491 7.62E-02 3.05E-02 114 57 57 0 0.637 3.75E-02 7.51E-03 RAN NVPNWHR 116 58 58 0 0.491 7.62E-02 3.05E-02 0 0 0 0 ND ND ND RAP2B EVSYGEGK 145 66 64 15 NA NA NA 0 0 0 0 ND ND ND
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Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
RAP2B VDLEGER 145 66 64 15 NA NA NA 145 66 64 15 NA NA NA S10A1 DVDAVDK 128 56 60 12 NA NA NA 128 56 60 12 NA NA NA S10A1 ELLQTELSGFLDAQK 128 56 60 12 NA NA NA 0 0 0 0 ND ND ND S10A6 ELTIGSK 154 70 71 13 0.974 7.42E-04 1.78E-03 154 70 71 13 0.978 5.77E-04 3.53E-04 S10A6 LQDAEIAR 154 70 71 13 0.974 7.42E-04 1.78E-03 0 0 0 0 0.989 1.92E-04 1.89E-04 SAA EANYIGSDK 143 65 63 15 NA NA NA 0 0 0 0 ND ND ND SAA SFFSFLGEAFDGAR 143 65 63 15 NA NA NA 143 65 63 15 1.000 9.15E-06 2.99E-05 SCF LFTPEEFFR 143 65 65 13 NA NA NA 143 65 65 13 0.630 3.88E-02 7.66E-03 SCF LVANLPK 143 65 65 13 NA NA NA 0 0 0 0 ND ND ND SEM3G DYPDEVLQFAR 155 70 71 14 NA NA NA 0 0 0 0 ND ND ND SEM3G LFLGGLDALYSLR 155 70 71 14 NA NA NA 155 70 71 14 0.874 5.76E-03 1.68E-03 SIAL AYEDEYSYFK 19 9 9 1 NA NA NA 19 9 9 1 NA NA NA SIAL TTSPPFGK 19 9 9 1 NA NA NA 0 0 0 0 ND ND ND SODM GDVTAQIALQPALK 154 69 71 14 0.156 4.45E-01 1.49E-01 151 67 70 14 0.168 4.24E-01 6.56E-02 SODM NVRPDYLK 154 69 71 14 0.156 4.45E-01 1.49E-01 3 2 1 0 0.615 4.19E-02 8.00E-03 SPON2 WSQTAFPK 63 30 31 2 NA NA NA 0 0 0 0 ND ND ND SPON2 YSITFTGK 63 30 31 2 NA NA NA 63 30 31 2 -
0.054 8.00E-01 1.19E-01
STAT1 TELISVSEVHPSR 38 18 17 3 NA NA NA 29 14 14 1 NA NA NA STAT1 YTYEHDPITK 38 18 17 3 NA NA NA 9 4 3 2 0.966 9.89E-04 4.69E-04 TBA1B AVFVDLEPTVIDEVR 119 60 56 3 NA NA NA 119 60 56 3 0.983 3.94E-04 2.97E-04 TBA1B EIIDLVLDR 119 60 56 3 NA NA NA 0 0 0 0 ND ND ND TBB3 ISVYYNEASSHK 158 72 71 15 0.123 5.05E-01 1.65E-01 158 72 71 15 0.991 1.10E-04 1.40E-04 TBB3 YLTVATVFR 158 72 71 15 0.123 5.05E-01 1.65E-01 0 0 0 0 0.349 1.71E-01 2.75E-02 TCPA IHPTSVISGYR 158 72 71 15 -
0.019 7.52E-01 2.35E-01 4 0 4 0 0.897 4.14E-03 1.32E-03
TCPA SSLGPVGLDK 158 72 71 15 - 7.52E-01 2.35E-01 154 72 67 15 0.705 2.66E-02 5.74E-03
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Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
0.019 TCPQ DIDEVSSLLR 48 24 23 1 NA NA NA 0 0 0 0 ND ND ND TCPQ NVGLDIEAEVPAVK 48 24 23 1 NA NA NA 48 24 23 1 NA NA NA TCPZ GIDPFSLDALSK 6 1 5 0 NA NA NA 6 1 5 0 NA NA NA TCPZ GLVLDHGAR 6 1 5 0 NA NA NA 0 0 0 0 ND ND ND TENA GLEPGQEYNVLLTAEK 140 67 61 12 NA NA NA 140 67 61 12 0.469 8.55E-02 1.47E-02 TENA TVSGNTVEYALTDLEPAT
EYTLR 140 67 61 12 NA NA NA 0 0 0 0 ND ND ND
TENX DAQGQPQAVPVSGDLR 158 72 71 15 0.705 2.66E-02 1.38E-02 158 72 71 15 0.795 1.46E-02 3.47E-03 TENX YEVTVVSVR 158 72 71 15 0.705 2.66E-02 1.38E-02 0 0 0 0 0.878 5.46E-03 1.62E-03 TERA GILLYGPPGTGK 106 53 52 1 0.799 1.43E-02 1.00E-02 94 48 45 1 0.862 7.07E-03 1.96E-03 TERA LDQLIYIPLPDEK 106 53 52 1 0.799 1.43E-02 1.00E-02 12 5 7 0 0.851 8.10E-03 2.23E-03 TETN GGTLSTPQTGSENDALYE
YLR 158 72 71 15 0.367 1.54E-01 5.69E-02 118 53 50 15 0.977 6.23E-04 3.74E-04
TETN LDTLAQEVALLK 158 72 71 15 0.367 1.54E-01 5.69E-02 40 19 21 0 0.984 3.57E-04 2.92E-04 TFR1 LTVSNVLK 157 71 71 15 0.752 2.02E-02 1.29E-02 0 0 0 0 0.625 3.97E-02 7.73E-03 TFR1 SSGLPNIPVQTISR 157 71 71 15 0.752 2.02E-02 1.29E-02 157 71 71 15 0.962 1.14E-03 5.18E-04 TIMP1 GFQALGDAADIR 151 70 69 12 NA NA NA 151 70 69 12 0.789 1.55E-02 3.59E-03 TIMP1 SEEFLIAGK 151 70 69 12 NA NA NA 0 0 0 0 ND ND ND TNF12 AAPFLTYFGLFQVH 156 71 71 14 NA NA NA 156 71 71 14 0.644 3.62E-02 7.30E-03 TNF12 INSSSPLR 156 71 71 14 NA NA NA 0 0 0 0 ND ND ND TPIS VVFEQTK 157 72 71 14 0.967 9.52E-04 1.78E-03 157 72 71 14 0.927 2.46E-03 9.06E-04 TPIS VVLAYEPVWAIGTGK 157 72 71 14 0.967 9.52E-04 1.78E-03 0 0 0 0 0.988 2.01E-04 1.91E-04 TRFL FQLFGSPSGQK 48 17 22 9 NA NA NA 22 7 11 4 NA NA NA TRFL LRPVAAEVYGTER 48 17 22 9 NA NA NA 4 1 3 0 0.908 3.36E-03 1.12E-03 TRFL VPSHAVVAR 48 17 22 9 NA NA NA 5 0 0 5 NA NA NA TRFL YYGYTGAFR 48 17 22 9 NA NA NA 17 9 8 0 NA NA NA
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Table S12. Protein and peptide detection in the discovery study.
Pro
tein
(H
UM
AN
)
Pep
tide
Pro
tein
det
ecti
on
Pro
tein
det
ecti
on
in c
ance
r
Pro
tein
det
ecti
on
in b
enig
n
Pro
tein
det
ecti
on
in H
PS
Pro
tein
co
rrel
atio
n
Pro
tein
p v
alue
Pro
tein
q v
alue
Pep
tide
det
ecti
on
Pep
tide
det
ecti
on
in c
ance
r
Pep
tide
det
ecti
on
in b
enig
n
Pep
tide
det
ecti
on
in H
PS
Pep
tide
co
rrel
atio
n
Pep
tide
p v
alue
Pep
tide
q v
alue
TSP1 GFLLLASLR 158 72 71 15 0.970 8.88E-04 1.78E-03 6 0 3 3 0.999 9.15E-06 2.99E-05 TSP1 GTSQNDPNWVVR 158 72 71 15 0.970 8.88E-04 1.78E-03 152 72 68 12 0.972 8.15E-04 4.13E-04 TTHY TSESGELHGLTTEEEFVEGI
YK 27 4 8 15 NA NA NA 27 4 8 15 0.996 1.83E-05 4.49E-05
TTHY VEIDTK 27 4 8 15 NA NA NA 0 0 0 0 ND ND ND TYPH ALQEALVLSDR 59 24 26 9 NA NA NA 0 0 0 0 ND ND ND TYPH TLVGVGASLGLR 59 24 26 9 NA NA NA 59 24 26 9 NA NA NA UGGG1 DLSQNFPTK 58 23 20 15 NA NA NA 58 23 20 15 NA NA NA UGGG1 FTILDSQGK 58 23 20 15 NA NA NA 0 0 0 0 ND ND ND UGPA LVEIAQVPK 97 49 45 3 NA NA NA 97 49 45 3 0.850 8.20E-03 2.23E-03 UGPA NENTFLDLTVQQIEHLNK 97 49 45 3 NA NA NA 0 0 0 0 ND ND ND VA0D1 LLFEGAGSNPGDK 13 1 0 12 NA NA NA 13 1 0 12 NA NA NA VA0D1 NVADYYPEYK 13 1 0 12 NA NA NA 0 0 0 0 ND ND ND VEGFC DLEEQLR 21 3 5 13 NA NA NA 21 3 5 13 NA NA NA VEGFC EAPAAAAAFESGLDLSDA
EPDAGEATAYASK 21 3 5 13 NA NA NA 0 0 0 0 ND ND ND
VEGFC FAAAHYNTEILK 21 3 5 13 NA NA NA 0 0 0 0 ND ND ND VEGFC NQPLNPGK 21 3 5 13 NA NA NA 0 0 0 0 ND ND ND VTNC AVRPGYPK 145 65 65 15 NA NA NA 0 0 0 0 ND ND ND VTNC DVWGIEGPIDAAFTR 145 65 65 15 NA NA NA 145 65 65 15 0.971 8.33E-04 4.15E-04 ZA2G EIPAWVPFDPAAQITK 158 72 71 15 NA NA NA 158 72 71 15 0.995 2.75E-05 6.22E-05 ZA2G WEAEPVYVQR 158 72 71 15 NA NA NA 0 0 0 0 ND ND ND
Note:
• Protein: UniProt protein name • Peptide: Peptide sequence
Submitted Manuscript: Confidential
115
• Protein detection: How many times the protein was detected in the 158 samples. It is also the sum of columns D, E and F. If any transition of the protein was detected in a sample, the protein was counted as detected in the sample. It is slightly higher than protein detection based on most intensive transition only.
• Protein detection in cancer: How many times the protein was detected in the 72 cancer samples. • Protein detection in benign: How many times the protein was detected in the 71 benign samples. • Protein detection in HPS: How many times the protein was detected in the 15 human plasma standard (HPS) samples. • Protein correlation: Pearson correlation between two peptides of the protein. Pearson coefficient was calculated between
tansitions having the highest median intensities of the corresponding peptides. If the two transitions were detected in less than five common samples, Pearson correlation was assigned to "NA".
• Protein p value: Empirical protein p value: See Supplementary Materials and Methods for more information. It was assigned to "NA" if the Pearson correlation was assigned to "NA".
• Protein q value: Protein q value: See Supplementary Materials and Methods for more information. It was assigned to "NA" if the Pearson correlation was assigned to "NA".
• Peptide detection: How many times the peptide was detected in the 158 samples. It is also the sum of columns K, L and M. If any transition of the peptide was detected in a sample, the peptide was counted as detected in the sample.
• Peptide detection in cancer: How many times the peptide was detected in the 72 cancer samples. • Peptide detection in benign: How many times the peptide was detected in the 71 benign samples. • Peptide detection in HPS: How many times the peptide was detected in the 15 HPS samples. • Peptide correlation: Pearson correlation between two transitions of the peptide. Pearson coefficient was calculated between
transitions having the highest median intensities of the peptide. If the two transitions were detected in less than five common samples, Pearson correlation was assigned to "NA". If the peptide was not detected, it was assigned to "ND".
• Peptide p value: Empirical peptide p value: See Supplementary Materials and Methods for more information. It was assigned to "NA" or "ND" if the Pearson correlation was assigned to "NA" or "ND".
• Peptide q value: Peptide q value: See Supplementary Materials and Methods for more information. It was assigned to "NA" or "ND" if the Pearson correlation was assigned to "NA" or "ND".