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Targeted Proteomics Environment Status of the Skyline open-source software project five years after...
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Targeted Proteomics Environment Status of the Skyline open-source software project five years after its inception Brendan MacLean
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Transcript of Targeted Proteomics Environment Status of the Skyline open-source software project five years after...
Targeted ProteomicsEnvironment
Status of the Skyline open-source software project five years after its inception
Brendan MacLean
User Community After 4 Years 560 registered users 150 registered for this meeting 4 new papers in May
Platform Independent and Label-free Quantitation of Proteomic Data using MS1 Extracted Ion Chromatograms in Skyline – Mol. Cel. Prot.
Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides – J. Prot. Res.
Using iRT, a Normalized Retention Time for More Targeted Measurement of Peptides - Proteomics
The Development of Selected Reaction Monitoring Methods for Targeted Proteomics via Empirical Refinement - Proteomics
25 abstracts at ASMS mention Skyline 75 citations of original paper (after 2 ½ years)
30 in 2012
User Community After 5 Years 1000+ registered users 250 registered for this meeting More papers and press
Targeted proteomics Nature Methods Method of the Year in 2012 MS1 Label-free Quantification Using Ion Intensity Chromatograms in
Skyline (Research and Clinical Applications) (book chapter) Design, Implementation, and Multi-Site Evaluation of a System
Suitability Protocol for the Quantitative Assessment of Instrument Performance in LC-MRM-MS - MCP
Viewing the Targeted Proteomics Horizon with Skyline – eProtein feature
37 abstracts at ASMS mention Skyline 200+ citations of original paper
Skyline Use
Dev 64 Release
Dev Release
1.3 Release1.2 Release1.1 ReleasePre-1.1 Release
1.3 64 Release
ASMS2010
ASMS2011
Skyline Instances Started Trailing 7 Days
Inst
ance
s
3500
3000
2500
1500
1000
500
0
2000
4000
4500
ASMS2012
5000
Panorama2013
Skyline Web Site Visits (past 3 months)
Learning More Au PS Workshop, Melbourne (February) US HUPO Workshop, Baltimore (March) Skyline User Group Meeting! here (now) SRM Course, Zurich (July) Proteomics Course, Cold Springs Harbor (July)
Targeted Quant. Course, Seattle
September 9-14
Instrument Vendor Partnerships
Panorama Partnership Program 2 – 4 labs Seeking leading edge targeted proteomics
infrastructure Local Panorama server installation Direct collaboration with Skyline/Panorama
team Full support for 1 year
Prior Knowledge and Consistency Powerful enough to be used cross-lab / cross
experiment More powerful run-to-run
Relative ion abundance Spectral and chromatogram libraries
Retention time iRT
Does ensuring comparable measurements require ID?
Haptoglobin L
ibra
ry
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
20
40
60
80
100
Pe
ak
Are
a P
erc
en
tag
e
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+y4 - 477.2304+ y3 - 363.1874+
Lib
rary
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
20
40
60
80
100
Pe
ak
Are
a P
erc
en
tag
e
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+y4 - 477.2304+ y3 - 363.1874+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
16.5
17.0
17.5
18.0
Re
ten
tio
n T
ime
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+y4 - 477.2304+ y3 - 363.1874+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
16.5
17.0
17.5
18.0
Re
ten
tio
n T
ime
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+y4 - 477.2304+ y3 - 363.1874+
LQTEGDGIYTLNSEK
Haptoglobin L
ibra
ry
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
2
4
6
8
Pe
ak
Are
a (
10
^6
)
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+ y4 - 477.2304+y3 - 363.1874+
Lib
rary
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
2
4
6
8
Pe
ak
Are
a (
10
^6
)
y13 - 1426.6696+ y9 - 1024.5310+ y7 - 854.4254+ y6 - 691.3621+ y4 - 477.2304+y3 - 363.1874+
LQTEGDGIYTLNSEK L
ibra
ry
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0.0
0.5
1.0
1.5
2.0
Pe
ak
Are
a (
10
^6
)
y7 - 757.4818+ y6 - 658.4134+ y5 - 543.3865+ y4 - 430.3024+
Lib
rary
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0.0
0.5
1.0
1.5
2.0
Pe
ak
Are
a (
10
^6
)
y7 - 757.4818+ y6 - 658.4134+ y5 - 543.3865+ y4 - 430.3024+
SVVDIGLIK
Mitochondrial 39S ribosomal protein L9D
_10
2_R
EP
1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
20
40
60
80
100
Pe
ak
Are
a P
erc
en
tag
e
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
20
40
60
80
100
Pe
ak
Are
a P
erc
en
tag
e
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
19.5
20.0
20.5
21.0
21.5
22.0
22.5
Re
ten
tio
n T
ime
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
19.5
20.0
20.5
21.0
21.5
22.0
22.5
Re
ten
tio
n T
ime
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
CSSLLWAGAAWLR
Mitochondrial 39S ribosomal protein L9D
_10
2_R
EP
1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
020406080
100120140
Pe
ak
Are
a (
10
^3
)
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
020406080
100120140
Pe
ak
Are
a (
10
^3
)
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
200
400
600
800
Pe
ak
Are
a (
10
^3
)
y9 - 961.5942+ y8 - 862.5257+ y6 - 664.3889+ y5 - 593.3518+ y4 - 496.2990+y3 - 359.2401+
D_
102
_RE
P1
D_
102
_RE
P2
D_
102
_RE
P3
D_
103
_RE
P1
D_
103
_RE
P2
D_
103
_RE
P3
D_
108
_RE
P1
D_
108
_RE
P2
D_
108
_RE
P3
D_
138
_RE
P1
D_
138
_RE
P2
D_
138
_RE
P3
D_
154
_RE
P1
D_
154
_RE
P2
D_
154
_RE
P3
D_
172
_RE
P1
D_
172
_RE
P2
D_
172
_RE
P3
D_
196
_RE
P1
D_
196
_RE
P2
D_
196
_RE
P3
H_
146
_RE
P1
H_
146
_RE
P2
H_
146
_RE
P3
H_
147
_RE
P1
H_
147
_RE
P2
H_
147
_RE
P3
H_
148
_RE
P1
H_
148
_RE
P2
H_
148
_RE
P3
H_
159
_RE
P1
H_
159
_RE
P2
H_
159
_RE
P3
H_
160
_RE
P1
H_
160
_RE
P2
H_
160
_RE
P3
H_
161
_RE
P1
H_
161
_RE
P2
H_
161
_RE
P3
H_
162
_RE
P1
H_
162
_RE
P2
H_
162
_RE
P3
Replicate
0
200
400
600
800
Pe
ak
Are
a (
10
^3
)
y9 - 961.5942+ y8 - 862.5257+ y6 - 664.3889+ y5 - 593.3518+ y4 - 496.2990+y3 - 359.2401+
SVVDIGLIK
CSSLLWAGAAWLR
CSSLLWAGAAWLRH_159_REP1
20.0 20.5 21.0 21.5
Retention Time
0
1000
2000
3000
4000
5000
Inte
ns
ity
20.7
21.6
20.4 20.6 20.8 21.0 21.2 21.4
Retention Time
0
20
40
60
80
100
120
140
Inte
ns
ity
21.0
21.4
D_138_REP3
18 19 20 21 22 23 24 25
Retention Time
0
100
200
300
400
500
600
700
800
900
Inte
ns
ity
21.0
22.5
23.119.4
22.8
20.0
19.6
D_1
02_R
EP
1
D_1
03_R
EP
1
D_1
08_R
EP
1
D_1
38_R
EP
1
D_1
54_R
EP
1
D_1
72_R
EP
1
D_1
96_R
EP
1
H_1
46_R
EP
1
H_1
47_R
EP
1
H_1
48_R
EP
1
H_1
59_R
EP
1
H_1
60_R
EP
1
H_1
61_R
EP
1
H_1
62_R
EP
1
D_1
02_R
EP
2
D_1
03_R
EP
2
D_1
08_R
EP
2
D_1
38_R
EP
2
D_1
54_R
EP
2
D_1
72_R
EP
2
D_1
96_R
EP
2
H_1
46_R
EP
2
H_1
47_R
EP
2
H_1
48_R
EP
2
H_1
59_R
EP
2
H_1
60_R
EP
2
H_1
61_R
EP
2
H_1
62_R
EP
2
D_1
02_R
EP
3
D_1
03_R
EP
3
D_1
08_R
EP
3
D_1
38_R
EP
3
D_1
54_R
EP
3
D_1
72_R
EP
3
D_1
96_R
EP
3
H_1
46_R
EP
3
H_1
47_R
EP
3
H_1
48_R
EP
3
H_1
59_R
EP
3
H_1
60_R
EP
3
H_1
61_R
EP
3
H_1
62_R
EP
3
Replicate
19.5
20.0
20.5
21.0
21.522.0
22.5
Re
ten
tio
n T
ime
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
D_1
02_R
EP
1
D_1
03_R
EP
1
D_1
08_R
EP
1
D_1
38_R
EP
1
D_1
54_R
EP
1
D_1
72_R
EP
1
D_1
96_R
EP
1
H_1
46_R
EP
1
H_1
47_R
EP
1
H_1
48_R
EP
1
H_1
59_R
EP
1
H_1
60_R
EP
1
H_1
61_R
EP
1
H_1
62_R
EP
1
D_1
02_R
EP
2
D_1
03_R
EP
2
D_1
08_R
EP
2
D_1
38_R
EP
2
D_1
54_R
EP
2
D_1
72_R
EP
2
D_1
96_R
EP
2
H_1
46_R
EP
2
H_1
47_R
EP
2
H_1
48_R
EP
2
H_1
59_R
EP
2
H_1
60_R
EP
2
H_1
61_R
EP
2
H_1
62_R
EP
2
D_1
02_R
EP
3
D_1
03_R
EP
3
D_1
08_R
EP
3
D_1
38_R
EP
3
D_1
54_R
EP
3
D_1
72_R
EP
3
D_1
96_R
EP
3
H_1
46_R
EP
3
H_1
47_R
EP
3
H_1
48_R
EP
3
H_1
59_R
EP
3
H_1
60_R
EP
3
H_1
61_R
EP
3
H_1
62_R
EP
3
Replicate
19.5
20.0
20.5
21.0
21.522.0
22.5
Re
ten
tio
n T
ime
y8 - 930.4944+ y7 - 744.4151+ y6 - 673.3780+ y5 - 616.3566+ y4 - 545.3194+y3 - 474.2823+
Truncated and Missing PeaksTGTNLMDFLSR
Deciphering the UnexpectedA
1A
3A
4A
5A
6A
7A
8A
9A
10
A11
A1
2B
1B
2B
3B
4B
5B
6B
7B
8B
10
B11
B1
2C
1C
2C
3C
4C
5C
6C
7C
8C
9C
10C
11C
12 D1
D2
D4
D5
D6
D7
D8
D9
D10
D11
D12 E
1E
2E
3E
4E
5E
6E
7E
8E
9E
10
E11
E1
2F
1F
2F
3F
4F
5F
6F
7F
8F
9F
10
F11
F1
2G
1G
2G
3G
4G
5G
6G
7G
8G
9G
10
G11
G1
2
Replicate
19.2
19.4
19.6
19.8
20.0
20.2
20.4
20.6
20.8
21.0
Re
ten
tio
n T
ime
YGQTIRPICLPCTEGTTR - 708.3506+++ YGQTIRPICLPCTEGTTR - 711.6867+++ (heavy)
A1
A3
A4
A5
A6
A7
A8
A9
A1
0A
11A
12
B1
B2
B3
B4
B5
B6
B7
B8
B1
0B
11B
12
C1
C2
C3
C4
C5
C6
C7
C8
C9
C10
C11
C12 D
1D
2D
4D
5D
6D
7D
8D
9D
10D
11D
12 E1
E2
E3
E4
E5
E6
E7
E8
E9
E1
0E
11E
12
F1
F2
F3
F4
F5
F6
F7
F8
F9
F1
0F
11F
12
G1
G2
G3
G4
G5
G6
G7
G8
G9
G1
0G
11G
12
Replicate
19.2
19.4
19.6
19.8
20.0
20.2
20.4
20.6
20.8
21.0
Re
ten
tio
n T
ime
YGQTIRPICLPCTEGTTR - 708.3506+++ YGQTIRPICLPCTEGTTR - 711.6867+++ (heavy) YGQTIRPICLPCTEGTTR
17 to 22-Feb-2012 16 to 17-Mar-2012
Aligned by iRTA
1A
3A
4A
5A
6A
7A
8A
9A
10
A11
A1
2B
1B
2B
3B
4B
5B
6B
7B
8B
10
B11
B1
2C
1C
2C
3C
4C
5C
6C
7C
8C
9C
10C
11C
12 D1
D2
D4
D5
D6
D7
D8
D9
D10
D11
D12 E1
E2
E3
E4
E5
E6
E7
E8
E9
E1
0E
11E
12
F1
F2
F3
F4
F5
F6
F7
F8
F9
F1
0F
11F
12
G1
G2
G3
G4
G5
G6
G7
G8
G9
G1
0G
11G
12
Replicate
37
38
39
40
41
42
43
iRT
(H
utt
en
ha
in)
Sc
ore
YGQTIRPICLPCTEGTTR - 708.3506+++ YGQTIRPICLPCTEGTTR - 711.6867+++ (heavy)
A1
A3
A4
A5
A6
A7
A8
A9
A1
0A
11A
12
B1
B2
B3
B4
B5
B6
B7
B8
B1
0B
11B
12
C1
C2
C3
C4
C5
C6
C7
C8
C9
C10
C11
C12 D
1D
2D
4D
5D
6D
7D
8D
9D
10D
11D
12 E1
E2
E3
E4
E5
E6
E7
E8
E9
E1
0E
11E
12
F1
F2
F3
F4
F5
F6
F7
F8
F9
F1
0F
11F
12
G1
G2
G3
G4
G5
G6
G7
G8
G9
G1
0G
11G
12
Replicate
37
38
39
40
41
42
43
iRT
(H
utt
en
ha
in)
Sc
ore
YGQTIRPICLPCTEGTTR - 708.3506+++ YGQTIRPICLPCTEGTTR - 711.6867+++ (heavy) YGQTIRPICLPCTEGTTR
Integrating with External Tools GeneSpring & Skyline Automation Tool
(Agilent) MSstats (Purdue) – Grouped study analysis QuaSAR (Broad Institute) – Response curves,
LOD, LOQ MS1 Probe (Buck Institute) – MS1 quant.
statistics TP28 – Alexandria D’Souza
SRM Collider (IMSB) – Interference probability calculator
External Tool MSstats
Replicate Annotations
Custom Reports
Analysis of reports with R – MSstats
Downstream Analysis with Statistical Tools
Skyline Automation with SkylineRunner
MS/MS Spectral Library Sources Global Proteome Machine NIST Peptide Atlas
Build your own from peptide search results Mascot MaxQuant Andromeda Morpheus Myrimatch / IDPicker OMSSA PRIDE XML Protein Pilot Protein Prospector
Proteome Discoverer (MSF) Scaffold – mzIdentML / MGF Spectrum Mill TPP – pepXML / mzXML files –
Peptide Atlas Waters Mse X! Tandem
Integrating Great Ideas (iRT)
Integrating Great Ideas (mProphet)
TP 499 - MacLean
Skyline Team Nick Shulman
Don Marsh
Kaipo Tamura
Danny Broudy Trevor Killeen
Vagish Sharma
Josh Eckels
Greg Taylor
Jarrett Egertson Dario Amodei
Collaborators: U. of Wa.
Eva Baker Jarrett Egertson Jimmy Eng Andrew Stergachis
Biognosys Lukas Reiter Oliver Rinner Claudia Escher
Broad Institute Sue Abbatiello Steve Carr Jake Jaffe D. R. Mani
Buck Institute Birgit Schilling Matthew Rardin Brad Gibson
Duke Will Thompson Arthur Moseley
IMSB Rudolph Aebersold Christina Ludwig Olga Schubert Hannes Röst Lucia Espona Pernas
Purdue Veavi Chang Meena Choi Olga Vitek
Stanford Dario Amodei Parag Mallick
Vanderbilt Matthew Chambers Daniel Liebler David Tabb
Instrument Vendor Support Agilent
Technologies Christine Miller Juli Salcedo Shripad Torvi Yinghang Yang
Bruker Carsten Baessmann Marius Kallhardt Stephanie Kaspar
AB Sciex David Cox Christie Hunter Brent Lefebvre
Thermo-Scientific Markus Kellmann Andreas Kuehn Vlad Zabrouskov
Waters Laurence Firth James Langridge Roy Martin Kieran Neeson Keith Richards
