Investigation into the Qualitative and Quantitative …€¦ · · 2007-11-21quantification of...
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TO DOWNLOAD A COPY OF THIS POSTER, VISIT WWW.WATERS.COM/POSTERS INTRODUCTION A variety of database search algorithms are available for the qualitative analysis of MALDI and ESI product ion MS/MS spectra. In most instances, these fragmentation spectra are acquired with data dependant acquisition methods and the algorithms tailored to accommodate the nature and characteristics of the data. Multiplexed, data independent acquisition fragmentation spectra can therefore pose a problem and are typically penalized because of their unexpected nature. The quantitative analysis of a (sub) proteome is often not adequately addressed but is becoming increasingly important. Label-free LC-MS experiments were conducted to investigate the quality of the results of a search algorithm – including absolute and relative quantitative analysis – for multiplexed LC-MS data sets. Previously characterized serum samples from four patients, prior to treatment, were depleted by removal of the six or twelve most abundant proteins. The samples were digested and analyzed by nanoscale LC-MS using a nano electrospray interface configured on a hybrid quadrupole/oa TOF mass spectrometer. Triplicate injections were performed for each sample and parallel qualitative and quantitative analysis of the obtained MS and multiplexed fragmentation spectra performed. Validation of the qualitative search results was conducted by means of the detailed analysis of a recombinant protein marker utilizing mass accuracy and time-alignment of the identified precursor and fragment ions. The quantitative aspects were validated by complementary analysis such as nanoscale LC - triple quadrupole MS/MS analysis and biochemical ELISA techniques. Investigation into the Qualitative and Quantitative Capabilities of a Database Search Algorithm for Alternate Scanning Multiplexed LC-MS Proteomics Data Johannes P.C. Vissers 1 , Guo-Zhong Li 2 , Catalin E. Doneanu 2 , Dan Golick 2 , Barry Dyson 1 , James I. Langridge 1 , Marc V. Gorenstein 2 , Jeffrey C. Silva 2 , Scott J. Geromanos 2 Waters Corporation, 1 MS Technologies Center, Manchester, UK and 2 Milford, Life Sciences Research and Development MA, USA Figure 1. The principle of multiplexed, alternate scanning (LC-MS E ) METHODS Sample preparation Pre treatment patient serum samples were diluted and solubilized prior to depletion with a affinity removal system (Agilent Technologies, Palo Alto, CA, USA or Beckman Coultar, Fullerton, CA, USA), which removes the six or twelve most abundant serum proteins, respectively. The depleted serum samples were subsequently denatured with RapiGest TM SF surfactant (0.1%) (Waters Corp.), reduced (10 mM DTT), alkylated (10 mM IAA) and enzymatically digested with trypsin, 1:50 (w/w) enzyme:protein ratio. LC-MS conditions Qualitative and quantitative LC-MS experiments were conducted using either a 1.5 or 0.5 hr reversed phase gradient from 5 to 40% acetonitrile (0.1% formic acid) at 250 nL/min on a nanoACQUITY UPLC TM System (Waters Corp.). An Atlantis ® 3μm C18 75 μm x 15 cm nanoscale LC column (Waters Corp.) was used, with all samples run in triplicate. Typical on-column sample loads were 0.5 μg protein digest. Multiplexed, alternate scanning (LC-MS E ) experiments — Figure 1 — were performed with a Q-Tof Premier TM mass spectrometer (Waters Corp.), which was programmed to step between normal (5 eV) and elevated (15-40 eV) collision energies applied to the gas cell, using a scan time of 1.5 seconds per function over the m/z range 50-1990. Triple quadrupole MS/MS experiments were conducted with a Quattro Premier XE mass spectrometer (Waters Corp.) in MRM mode of analysis. The transmission window of both mass analyzers was typically 1 Da, the dwell time 25 ms and the collision energy approximately 20 eV. ELISA Chitinase-1 activity was measured with 4-methylumbelliferyl β- D-N,N’,N”-triacetylchitotriose as substrate at pH 5.2 References 1. Vissers, J.P.C., Langridge J.I., Aerts, J.M.F.G. (2007) Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease,, Mol. Cell. Proteomics 6, 755-766 2. Silva, J.C., Denny R., Dorschel, C.A., Gorenstein, M., Kass, I.J., Li, G.-Z., McKenna, T., Nold, M.J., Richardson, K., Young P., and Geromanos, S. (2005) Quantitative proteomic analysis by accurate mass retention time pairs, Anal. Chem. 77, 2187-2200 3. Silva, J.C., Gorenstein, M.V., Li, G.-Z., Vissers, J.P.C., Geromanos, S.J. (2006) Absolute quantification of proteins by LCMS E ; a virtue of parallel MS acquisition, Mol. Cell. Proteomics 5, 144-156 4. Aerts, J.M.F.G., Donker-Koopman, W.E., Koot, M., Barranger, J.A., Tager, J.M., and Schram, A.W. (1986) Deficient activity of glucocerebrosidase in urine from patients with type 1 Gaucher disease. Clin. Chim. Acta 158, 155-164 5. Hollak, C.E.M., van Weely, S., van Oers, M.H.J., and Aerts, J.M.F.G. (1994) Marked elevation of plasma chitotriosidase activity; a novel hallmark of Gaucher disease, J. Clin. Invest. 93, 1288-1292 Search Algorithm Protein identifications and quantitative information were generated by the use of dedicated algorithms (Identity E , Waters Corp.), and searching against a human species-specific database. The principle and workflow of the search algorithm is illustrated in Figure 2 RESULTS Precursor and fragment ion maps Chitinase-1 is a marker protein for deficiency in the human glycosphingolipid catabolism pathway. The protein was recombinantly expressed and analyzed in its tryptic digested form to create a so-called ion map of all precursor and fragment ions that can be identified to this protein — Figure 3. Figure 7. Chitinase-1 activity determined by ELISA (n = 1; 5% method error), LC-MS E (n = 3) and MRM LC-MS/MS (n = 3) for four independent glucocerebrosidase deficiency patients CONCLUSION • A specific glucocerebrosidase deficiency biomarker — Chitinase 1 — has been positively identified, quantified and its enzyme activity determined • Ion maps — including retention time and relative intensities of both precursor and fragment ions — allowed for the search validation and confirmation of sub fmol levels of Chitinase-1 in the presence of 0.5 μg depleted serum • Independent quantitative methods — ELISA and triple quadrupole MRM LC-MS/MS analysis — confirmed the determined amounts, concentrations and enzyme activities for all investigated patient pretreatment samples [ ] standard internal standard internal intensity peptide normalized x protein intensity peptide normalized n 1 i n 1 i ⋅ ∑ ∑ = = Figure 2. Workflow of the Identity E search algorithm — see poster WPQ–275 for algorithm details Absolute quantification The concentration and on-column amounts of Chitinase-1 for the LC-MS E experiments was determined by means of the fol- lowing formula for all four investigated patients: The results of the alternate scanning multiplexed LC-MS E ex- periments were also used to develop and optimize quantitative triple quadrupole LC-MS/MS analysis — see Figure 6. Figure 3. Ion map precursor (top) and fragment ions (bottom) of recombinant Chitinase-1 Figure 4. Alternate scanning multiplexed LC-MS E identification of Chitinase-1 Chitinase-1 was positively identified in the depleted serum of four pre-treatment patients. The observed ion maps — precur- sor and fragments distributions — were compared with the re- sults obtained for recombinant Chitinase-1 — Figures 4 and 5 Figure 6. Identity E discovery/MRM quantification workflow — see poster MPZ6-499 for detail on peptide MRM optimization strategies Label Label-Free Free Quantitative Quantitative Analysis Analysis Pre Pre-selection/transitions selection/transitions MRM candidates MRM candidates Cone Voltage and Cone Voltage and Collision Energy Collision Energy Optimization Optimization 1. Confirmative analysis 2. Absolute quantification LS LS-MS MS E Identity Identity E db search db search Label Label-Free Free Quantitative Quantitative Analysis Analysis Pre Pre-selection/transitions selection/transitions MRM candidates MRM candidates Cone Voltage and Cone Voltage and Collision Energy Collision Energy Optimization Optimization Discovery Discovery QQQ QQQ QuanLynx QuanLynx Quantification Quantification 1. Confirmative analysis 2. Absolute quantification Figure 5. Time and relative intensity distribution maps T17 peptide recombinant Chitinase-1 and native pretreatment hu- man serum Chitinase-1 Table 1 summarizes the ELISA activity measurements and the quantitative LC-MS analysis by means of nanoscale LC-MS E al- ternate scanning and triple quadrupole LC-MS/MS MRM — 2 peptides; 2 transitions/peptide — analysis. Figure 7 illustrates a comparison of the 3 applied techniques to determine Chitinase-1 activity of pretreatment serum samples of glucocerebrosidase deficiency patients. The LC-MS deter- mined concentration levels were converted to activity units. Table 1. Chitinase-1 activity (ELISA 1 ) and LC-MS determined concentrations (LC-MS E,2 and MRM 3 ); * n = 1 (5% method er- ror); ** different original sample dilutions; n = 3 patient activity 1 (nmol/mL h)* concentration 2 (fmol/μL)** concentration 3 (fmol/μL)** A B C D 31,800 ± 1590 15,900 ± 800 62,100 ± 3100 20,400 ± 1020 1.59 ± 0.31 0.99 ± 0.16 1.59 ± 0.18 1.01 ± 0.05 NA 2.8 ± 0.2 10.4 ±0.4 4.4 ± 0.1 Read in Calculated MH + Values from Precursor Product Ion Table Typical Search Parameters 1.Delta RT (LE – HE) 2.10 ppm Precursor 3.20 ppm Product Ion 4.Minimum Product Ion to Match 1. Most Product Ions to Match 2. Consecutive y”/b ions to match 3. Correct Number of Product Ions by Length, Charge-State, & Intensity - Model 4. Presence of Preferred Fragmentation Site(s) - Model 5. Sum y”/b ion intensity Ratio - Model Collapse all Tentative Peptide Identifications into Proteins Only the Tentative Peptide Identifications that are the Highest Ranked for each LE EMRT Contribute Data to the Initial Protein Rank Read in Calculated MH + Values from Precursor Product Ion Table Typical Search Parameters 1.Delta RT (LE – HE) 2.10 ppm Precursor 3.20 ppm Product Ion 4.Minimum Product Ion to Match 1. Most Product Ions to Match 2. Consecutive y”/b ions to match 3. Correct Number of Product Ions by Length, Charge-State, & Intensity - Model 4. Presence of Preferred Fragmentation Site(s) - Model 5. Sum y”/b ion intensity Ratio - Model Collapse all Tentative Peptide Identifications into Proteins Only the Tentative Peptide Identifications that are the Highest Ranked for each LE EMRT Contribute Data to the Initial Protein Rank T17 - FTTLVQDLANAFQQEAQTSGK Fragment ion intensity distribution Precursor and fragment ion elution times 0 10000 20000 30000 40000 50000 60000 70000 A B C D pat ient ELISA LC-MS E MRM Fragment Ion Map Elevated Energy LC-MS E Function Precursor Ion Map Low Energy LC-MS E Function ion type 0 10 20 30 40 50 60 70 80 precursor y"6 y"7 y"8 y"9 74.02 73.92 73.97 73.93 74.03 73.92 73.99 73.94 74.04 73.93 native recombinant retention time (min) intensity ratio Y"6/y"9 Y"7/y"9 Y"8/y"9 Y"9/y"9 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 native recombinant relative fragment ion intensity Retention time m/z Retention time m/z Retention time m/z Retention time m/z Retention time m/z Retention time m/z 720002231EN
Transcript of Investigation into the Qualitative and Quantitative …€¦ · · 2007-11-21quantification of...
TO DOWNLOAD A COPY OF THIS POSTER, VISIT WWW.WATERS.COM/POSTERS
INTRODUCTION A variety of database search algorithms are available for the qualitative analysis of MALDI and ESI product ion MS/MS spectra. In most instances, these fragmentation spectra are acquired with data dependant acquisition methods and the algorithms tailored to accommodate the nature and characteristics of the data. Multiplexed, data independent acquisition fragmentation spectra can therefore pose a problem and are typically penalized because of their unexpected nature. The quantitative analysis of a (sub) proteome is often not adequately addressed but is becoming increasingly important. Label-free LC-MS experiments were conducted to investigate the quality of the results of a search algorithm – including absolute and relative quantitative analysis – for multiplexed LC-MS data sets.
Previously characterized serum samples from four patients, prior to treatment, were depleted by removal of the six or twelve most abundant proteins. The samples were digested and analyzed by nanoscale LC-MS using a nano electrospray interface configured on a hybrid quadrupole/oa TOF mass spectrometer. Triplicate injections were performed for each sample and parallel qualitative and quantitative analysis of the obtained MS and multiplexed fragmentation spectra performed. Validation of the qualitative search results was conducted by means of the detailed analysis of a recombinant protein marker utilizing mass accuracy and time-alignment of the identified precursor and fragment ions. The quantitative aspects were validated by complementary analysis such as nanoscale LC - triple quadrupole MS/MS analysis and biochemical ELISA techniques.
Investigation into the Qualitative and Quantitative Capabilities of a Database Search Algorithm for Alternate Scanning Multiplexed LC-MS Proteomics Data Johannes P.C. Vissers1, Guo-Zhong Li2, Catalin E. Doneanu2, Dan Golick2, Barry Dyson1, James I. Langridge1, Marc V. Gorenstein2, Jeffrey C. Silva2, Scott J. Geromanos2 Waters Corporation, 1 MS Technologies Center, Manchester, UK and 2Milford, Life Sciences Research and Development MA, USA
Figure 1. The principle of multiplexed, alternate scanning (LC-MSE)
METHODS Sample preparation
Pre treatment patient serum samples were diluted and solubilized prior to depletion with a affinity removal system (Agilent Technologies, Palo Alto, CA, USA or Beckman Coultar, Fullerton, CA, USA), which removes the six or twelve most abundant serum proteins, respectively. The depleted serum samples were subsequently denatured with RapiGestTM SF surfactant (0.1%) (Waters Corp.), reduced (10 mM DTT), alkylated (10 mM IAA) and enzymatically digested with trypsin, 1:50 (w/w) enzyme:protein ratio. LC-MS conditions
Qualitative and quantitative LC-MS experiments were conducted using either a 1.5 or 0.5 hr reversed phase gradient from 5 to 40% acetonitrile (0.1% formic acid) at 250 nL/min on a nanoACQUITY UPLCTM System (Waters Corp.). An Atlantis® 3µm C18 75 µm x 15 cm nanoscale LC column (Waters Corp.) was used, with all samples run in triplicate. Typical on-column sample loads were 0.5 µg protein digest. Multiplexed, alternate scanning (LC-MSE) experiments — Figure 1 — were performed with a Q-Tof PremierTM mass spectrometer (Waters Corp.), which was programmed to step between normal (5 eV) and elevated (15-40 eV) collision energies applied to the gas cell, using a scan time of 1.5 seconds per function over the m/z range 50-1990. Triple quadrupole MS/MS experiments were conducted with a Quattro Premier XE mass spectrometer (Waters Corp.) in MRM mode of analysis. The transmission window of both mass analyzers was typically 1 Da, the dwell time 25 ms and the collision energy approximately 20 eV. ELISA
Chitinase-1 activity was measured with 4-methylumbelliferyl β-D-N,N’,N”-triacetylchitotriose as substrate at pH 5.2
References
1. Vissers, J.P.C., Langridge J.I., Aerts, J.M.F.G. (2007) Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease,, Mol. Cell. Proteomics 6, 755-766
2. Silva, J.C., Denny R., Dorschel, C.A., Gorenstein, M., Kass, I.J., Li, G.-Z., McKenna, T., Nold, M.J., Richardson, K., Young P., and Geromanos, S. (2005) Quantitative proteomic analysis by accurate mass retention time pairs, Anal. Chem. 77, 2187-2200
3. Silva, J.C., Gorenstein, M.V., Li, G.-Z., Vissers, J.P.C., Geromanos, S.J. (2006) Absolute quantification of proteins by LCMSE; a virtue of parallel MS acquisition, Mol. Cell. Proteomics 5, 144-156
4. Aerts, J.M.F.G., Donker-Koopman, W.E., Koot, M., Barranger, J.A., Tager, J.M., and Schram, A.W. (1986) Deficient activity of glucocerebrosidase in urine from patients with type 1 Gaucher disease. Clin. Chim. Acta 158, 155-164
5. Hollak, C.E.M., van Weely, S., van Oers, M.H.J., and Aerts, J.M.F.G. (1994) Marked elevation of plasma chitotriosidase activity; a novel hallmark of Gaucher disease, J. Clin. Invest. 93, 1288-1292
Search Algorithm
Protein identifications and quantitative information were generated by the use of dedicated algorithms (IdentityE, Waters Corp.), and searching against a human species-specific database. The principle and workflow of the search algorithm is illustrated in Figure 2
RESULTS Precursor and fragment ion maps
Chitinase-1 is a marker protein for deficiency in the human glycosphingolipid catabolism pathway. The protein was recombinantly expressed and analyzed in its tryptic digested form to create a so-called ion map of all precursor and fragment ions that can be identified to this protein — Figure 3.
Figure 7. Chitinase-1 activity determined by ELISA (n = 1; 5% method error), LC-MSE (n = 3) and MRM LC-MS/MS (n = 3) for four independent glucocerebrosidase deficiency patients
CONCLUSION
• A specific glucocerebrosidase deficiency biomarker —Chitinase 1 — has been positively identified, quantified and its enzyme activity determined
• Ion maps — including retention time and relative
intensities of both precursor and fragment ions — allowed for the search validation and confirmation of sub fmol levels of Chitinase-1 in the presence of 0.5 µg depleted serum
• Independent quantitative methods — ELISA and triple
quadrupole MRM LC-MS/MS analysis — confirmed the determined amounts, concentrations and enzyme activities for all investigated patient pretreatment samples
[ ]standard internalstandard internalintensity peptide normalized
xproteinintensity peptide normalizedn
1i
n
1i ⋅∑
∑
=
=
Figure 2. Workflow of the IdentityE search algorithm — see poster WPQ–275 for algorithm details
Absolute quantification
The concentration and on-column amounts of Chitinase-1 for the LC-MSE experiments was determined by means of the fol-lowing formula for all four investigated patients: The results of the alternate scanning multiplexed LC-MSE ex-periments were also used to develop and optimize quantitative triple quadrupole LC-MS/MS analysis — see Figure 6.
Figure 3. Ion map precursor (top) and fragment ions (bottom) of recombinant Chitinase-1
Figure 4. Alternate scanning multiplexed LC-MSE identification of Chitinase-1
Chitinase-1 was positively identified in the depleted serum of four pre-treatment patients. The observed ion maps — precur-sor and fragments distributions — were compared with the re-sults obtained for recombinant Chitinase-1 — Figures 4 and 5
Figure 6. IdentityE discovery/MRM quantification workflow — see poster MPZ6-499 for detail on peptide MRM optimization strategies
LSLS--MSMSEE IdentityIdentityEE
db searchdb search
LabelLabel--FreeFreeQuantitativeQuantitative
AnalysisAnalysis
PrePre--selection/transitionsselection/transitionsMRM candidatesMRM candidates
Cone Voltage andCone Voltage andCollision EnergyCollision Energy
OptimizationOptimization
DiscoveryDiscovery
QQQQQQ QuanLynxQuanLynx
QuantificationQuantification
1. Confirmative analysis2. Absolute quantification
LSLS--MSMSEE IdentityIdentityEE
db searchdb search
LabelLabel--FreeFreeQuantitativeQuantitative
AnalysisAnalysis
PrePre--selection/transitionsselection/transitionsMRM candidatesMRM candidates
Cone Voltage andCone Voltage andCollision EnergyCollision Energy
OptimizationOptimization
DiscoveryDiscovery
QQQQQQ QuanLynxQuanLynx
QuantificationQuantification
1. Confirmative analysis2. Absolute quantification
Figure 5. Time and relative intensity distribution maps T17 peptide recombinant Chitinase-1 and native pretreatment hu-man serum Chitinase-1
Table 1 summarizes the ELISA activity measurements and the quantitative LC-MS analysis by means of nanoscale LC-MSE al-ternate scanning and triple quadrupole LC-MS/MS MRM — 2 peptides; 2 transitions/peptide — analysis. Figure 7 illustrates a comparison of the 3 applied techniques to determine Chitinase-1 activity of pretreatment serum samples of glucocerebrosidase deficiency patients. The LC-MS deter-mined concentration levels were converted to activity units.
Table 1. Chitinase-1 activity (ELISA1) and LC-MS determined concentrations (LC-MSE,2 and MRM3); * n = 1 (5% method er-ror); ** different original sample dilutions; n = 3
patient activity1 (nmol/mL h)*
concentration2 (fmol/µL)**
concentration3
(fmol/µL)**
A B C D
31,800 ± 1590 15,900 ± 800 62,100 ± 3100 20,400 ± 1020
1.59 ± 0.31 0.99 ± 0.16 1.59 ± 0.18 1.01 ± 0.05
NA 2.8 ± 0.2 10.4 ±0.4 4.4 ± 0.1
Read in Calculated MH+ Values from Precursor Product Ion Table
Typical Search Parameters1.Delta RT (LE – HE)2.10 ppm Precursor3.20 ppm Product Ion4.Minimum Product Ion to Match
1. Most Product Ions to Match2. Consecutive y”/b ions to match3. Correct Number of Product Ions by
Length, Charge-State, & Intensity - Model4. Presence of Preferred Fragmentation
Site(s) - Model5. Sum y”/b ion intensity Ratio - Model
Collapse all Tentative Peptide Identifications into Proteins
Only the Tentative Peptide Identifications that are the Highest Ranked for each LE EMRT Contribute Data to the Initial Protein Rank
Read in Calculated MH+ Values from Precursor Product Ion Table
Typical Search Parameters1.Delta RT (LE – HE)2.10 ppm Precursor3.20 ppm Product Ion4.Minimum Product Ion to Match
1. Most Product Ions to Match2. Consecutive y”/b ions to match3. Correct Number of Product Ions by
Length, Charge-State, & Intensity - Model4. Presence of Preferred Fragmentation
Site(s) - Model5. Sum y”/b ion intensity Ratio - Model
Collapse all Tentative Peptide Identifications into Proteins
Only the Tentative Peptide Identifications that are the Highest Ranked for each LE EMRT Contribute Data to the Initial Protein Rank
T17 - FTTLVQDLANAFQQEAQTSGK
Fragment ion intensity distribution
Precursor and fragment ion elution times
0
10000
20000
30000
40000
50000
60000
70000
A B C D
pat ient
ELISA
LC-MSE
MRM
Fragment Ion Map Elevated Energy LC-MSE Function
Precursor Ion Map Low Energy LC-MSE Function
ion type
0
10
20
30
40
50
60
70
80
precursor y"6 y"7 y"8 y"9
74
.02
73
.92
73
.97
73
.93
74
.03
73
.92
73
.99
73
.94
74
.04
73
.93
native
recombinant
rete
ntion t
ime
(min
)
intensity ratio
Y"6/y"9
Y"7/y"9
Y"8/y"9
Y"9/y"9
0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2
native
recombinant
rela
tive
fra
gm
ent
ion inte
nsi
ty
Retention time
m/z
Retention time
m/z
Retention time
m/z
Retention time
m/z
Retention time
m/z
Retention time
m/z
720002231EN
