RAF1, CPTAC-1335 - CPTAC Assay Portal (original) (raw)
Please include the following statement when referencing the CPTAC Assay Portal
We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.
Protein Sequence hover to view complete sequence
CPTAC-5778: View additional GYASPDLSK data
non-CPTAC-5570: View additional GYASPDLSK data
CPTAC-1546: View additional TISNGFGFK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MEHIQGAWKT | ISNGFGFKDA | VFDGSSCISP | TIVQQFGYQR | RASDDGKLTD |
| 60 | 70 | 80 | 90 | 100 |
| PSKTSNTIRV | FLPNKQRTVV | NVRNGMSLHD | CLMKALKVRG | LQPECCAVFR |
| 110 | 120 | 130 | 140 | 150 |
| LLHEHKGKKA | RLDWNTDAAS | LIGEELQVDF | LDHVPLTTHN | FARKTFLKLA |
| 160 | 170 | 180 | 190 | 200 |
| FCDICQKFLL | NGFRCQTCGY | KFHEHCSTKV | PTMCVDWSNI | RQLLLFPNST |
| 210 | 220 | 230 | 240 | 250 |
| IGDSGVPALP | SLTMRRMRES | VSRMPVSSQH | RYSTPHAFTF | NTSSPSSEGS |
| 260 | 270 | 280 | 290 | 300 |
| LSQRQRSTST | PNVHMVSTTL | PVDSRMIEDA | IRSHSESASP | SALSSSPNNL |
| 310 | 320 | 330 | 340 | 350 |
| SPTGWSQPKT | PVPAQRERAP | VSGTQEKNKI | RPRGQRDSSY | YWEIEASEVM |
| 360 | 370 | 380 | 390 | 400 |
| LSTRIGSGSF | GTVYKGKWHG | DVAVKILKVV | DPTPEQFQAF | RNEVAVLRKT |
| 410 | 420 | 430 | 440 | 450 |
| RHVNILLFMG | YMTKDNLAIV | TQWCEGSSLY | KHLHVQETKF | QMFQLIDIAR |
| 460 | 470 | 480 | 490 | 500 |
| QTAQGMDYLH | AKNIIHRDMK | SNNIFLHEGL | TVKIGDFGLA | TVKSRWSGSQ |
| 510 | 520 | 530 | 540 | 550 |
| QVEQPTGSVL | WMAPEVIRMQ | DNNPFSFQSD | VYSYGIVLYE | LMTGELPYSH |
| 560 | 570 | 580 | 590 | 600 |
| INNRDQIIFM | VGRGYASPDL | SKLYKNCPKA | MKRLVADCVK | KVKEERPLFP |
| 610 | 620 | 630 | 640 | 648 |
| QILSSIELLQ | HSLPKINRSA | SEPSLHRAAH | TEDINACTLT | TSPRLPVF |
Data source: UniProt
Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs
Uniprot Database Entry PhosphoSitePlus ®
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Phosphorylation Acetylation Ubiquitylation Other
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Assay Details for CPTAC-1335 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
AS[+80.0]DDGKLTDPSK
Modification Type
Phospho (ST)
Protein - Site of Modification
43
Peptide - Site of Modification
2
Peptide Start
42
Peptide End
53
CPTAC ID
CPTAC-1335
Peptide Molecular Mass
1,312.5548
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Digested Cell Lysate
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
medium stable isotope peptide (delta 6 amu)
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C at C-terminus K
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 3 um, 200A
Column Dimensions
0.075 x 100 mm
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV
| n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y6 (1+) | 11.1 | 9.2 | 10.1 | 9.8 | 10.1 | 10.8 | 14.8 | 13.7 | 14.8 | 15 | 15 | 15 |
| y5 (1+) | 13.3 | 8.6 | 12 | 12.4 | 9.1 | 16.1 | 18.2 | 12.5 | 20.1 | 15 | 15 | 15 |
| b4-98 (1+) | 12.9 | 10.4 | 12.8 | 14.4 | 13.2 | 15 | 19.3 | 16.8 | 19.7 | 15 | 15 | 15 |
| sum | 6.6 | 6.1 | 8.2 | 7.6 | 6.2 | 11 | 10.1 | 8.7 | 13.7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1336 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
SAS[+80.0]EPSLHR
Modification Type
Phospho (ST)
Protein - Site of Modification
621
Peptide - Site of Modification
3
Peptide Start
619
Peptide End
627
CPTAC ID
CPTAC-1336
Peptide Molecular Mass
1,062.4495
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Digested Cell Lysate
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
medium stable isotope peptide (delta 6 amu)
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 3 um, 200A
Column Dimensions
0.075 x 100 mm
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y6 (1+) | 17.2 | 13.1 | 7.7 | 13.8 | 18.3 | 13.1 | 22.1 | 22.5 | 15.2 | 15 | 15 | 15 |
| y5 (1+) | 5 | 5.2 | 5.6 | 8.1 | 6.8 | 10.5 | 9.5 | 8.6 | 11.9 | 15 | 15 | 15 |
| b4-98 (1+) | 22.4 | 14.1 | 12.1 | 26.4 | 20.4 | 17.9 | 34.6 | 24.8 | 21.6 | 15 | 15 | 15 |
| sum | 6.8 | 3.2 | 5.6 | 10.1 | 5.4 | 10.5 | 12.2 | 6.3 | 11.9 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-5780 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
GLQPEC[+57.021464]C[+57.021464]AVFR
Modification Type
Carbamidomethyl (C)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
90
Peptide End
100
CPTAC ID
CPTAC-5780
Peptide Molecular Mass
1,335.6064
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center, H. Lee Moffitt Cancer Center & Research Institute, Broad Institute
Submitting Lab PI
Amanda Paulovich, John Koomen, Steven A. Carr
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
SCIEX 5500 / Thermo Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y6 (1+) | 26.3 | 14.3 | 8.5 | 24.9 | 30.6 | 16.4 | 36.2 | 33.8 | 18.5 | 15 | 15 | 15 |
| y7 (1+) | 32.3 | 17.6 | 9 | 35.2 | 32.8 | 13.4 | 47.8 | 37.2 | 16.1 | 15 | 15 | 15 |
| y8 (1+) | 20.1 | 12.7 | 6.3 | 29.7 | 30.2 | 14.3 | 35.9 | 32.8 | 15.6 | 15 | 15 | 15 |
| sum | 19.1 | 12.7 | 6.5 | 26.9 | 30.2 | 14.3 | 33 | 32.8 | 15.7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-5778 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
GYASPDLSK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
564
Peptide End
572
CPTAC ID
CPTAC-5778
Peptide Molecular Mass
936.4553
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center, H. Lee Moffitt Cancer Center & Research Institute, Broad Institute
Submitting Lab PI
Amanda Paulovich, John Koomen, Steven A. Carr
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
SCIEX 5500 / Thermo Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 21.1 | 10.6 | 7.5 | 24.6 | 26 | 16.3 | 32.4 | 28.1 | 17.9 | 15 | 15 | 15 |
| y6 (1+) | 18.6 | 11.7 | 6.8 | 24.7 | 29.5 | 17.7 | 30.9 | 31.7 | 19 | 15 | 15 | 15 |
| y7 (1+) | 19.3 | 12.2 | 5.5 | 24.8 | 29.5 | 16.1 | 31.4 | 31.9 | 17 | 15 | 15 | 15 |
| sum | 18.5 | 11.6 | 6.2 | 24.1 | 28.7 | 16.5 | 30.4 | 31 | 17.6 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-5828 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
STSTPNVHMVSTTLPVDSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
257
Peptide End
275
CPTAC ID
CPTAC-5828
Peptide Molecular Mass
2,027.9946
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center, H. Lee Moffitt Cancer Center & Research Institute, Broad Institute
Submitting Lab PI
Amanda Paulovich, John Koomen, Steven A. Carr
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
SCIEX 5500 / Thermo Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 20.9 | 12.8 | 7.1 | 28.5 | 23.3 | 11.4 | 35.3 | 26.6 | 13.4 | 16 | 15 | 17 |
| y6 (1+) | 19.9 | 9.6 | 11.2 | 19.6 | 17.4 | 17.5 | 27.9 | 19.9 | 20.8 | 16 | 15 | 17 |
| y7 (1+) | 25 | 12.4 | 15.9 | 31.6 | 21.8 | 22.5 | 40.3 | 25.1 | 27.6 | 16 | 15 | 17 |
| sum | 21.3 | 12.8 | 7.1 | 28.8 | 23.7 | 11.9 | 35.8 | 26.9 | 13.9 | 16 | 15 | 17 |
Additional Resources and Comments
Assay Details for CPTAC-5829 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
STS[+79.966331]TPNVHMVSTTLPVDSR
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
257
Peptide End
275
CPTAC ID
CPTAC-5829
Peptide Molecular Mass
2,107.9609
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center, H. Lee Moffitt Cancer Center & Research Institute, Broad Institute
Submitting Lab PI
Amanda Paulovich, John Koomen, Steven A. Carr
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
SCIEX 5500 / Thermo Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 6.8 | 7.3 | 5.3 | 11.2 | 12.4 | 12.8 | 13.1 | 14.4 | 13.9 | 16 | 15 | 16 |
| y15 (2+) | 6 | 7.5 | 4.6 | 9.8 | 13.2 | 10.9 | 11.5 | 15.2 | 11.8 | 16 | 15 | 16 |
| sum | 6.6 | 7.3 | 4.7 | 10.9 | 12.5 | 12.1 | 12.7 | 14.5 | 13 | 16 | 15 | 16 |
Additional Resources and Comments
Assay Details for CPTAC-5779 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
VVDPTPEQFQAFR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
379
Peptide End
391
CPTAC ID
CPTAC-5779
Peptide Molecular Mass
1,532.7623
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center, H. Lee Moffitt Cancer Center & Research Institute, Broad Institute
Submitting Lab PI
Amanda Paulovich, John Koomen, Steven A. Carr
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
SCIEX 5500 / Thermo Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y8 (1+) | 22.3 | 12.4 | 11.8 | 25.4 | 32.1 | 16.3 | 33.8 | 34.4 | 20.1 | 15 | 15 | 15 |
| y10 (1+) | 29.9 | 8.6 | 11.5 | 25.4 | 33.2 | 16.3 | 39.2 | 34.3 | 19.9 | 15 | 15 | 15 |
| sum | 23.9 | 11.4 | 11.7 | 25.1 | 32.2 | 16.3 | 34.7 | 34.2 | 20.1 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5433 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
DSSYYWEIEASEVMLSTR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
337
Peptide End
354
CPTAC ID
non-CPTAC-5433
Peptide Molecular Mass
2,164.9623
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Cell Lysate
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
RSLCnano and Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y8 (1+) | 63.6 | 50 | 13.2 | 50.8 | 36.7 | 31.4 | 81.4 | 62 | 34.1 | 15 | 15 | 15 |
| y10 (1+) | 58.5 | 40.9 | 11.7 | 55.2 | 40.4 | 23.2 | 80.4 | 57.5 | 26 | 15 | 15 | 15 |
| y11 (1+) | 80.8 | 51.1 | 15.2 | 58.5 | 32.6 | 27.2 | 99.8 | 60.6 | 31.2 | 15 | 15 | 15 |
| sum | 66.5 | 45.1 | 7.9 | 51.4 | 33.9 | 25.4 | 84 | 56.4 | 26.6 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5431 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
GLQPEC[+57.021464]C[+57.021464]AVFR
Modification Type
Carbamidomethyl (C), Carbamidomethyl (C)
Protein - Site of Modification
96, 97
Peptide - Site of Modification
6, 7
Peptide Start
90
Peptide End
100
CPTAC ID
non-CPTAC-5431
Peptide Molecular Mass
1,335.6064
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Cell Lysate
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
RSLCnano and Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y7 (1+) | 13.4 | 5.2 | 4.1 | 15.1 | 5 | 6.2 | 20.2 | 7.2 | 7.4 | 15 | 15 | 15 |
| y8 (1+) | 4.2 | 1.6 | 2.8 | 5.4 | 2.7 | 3.2 | 6.8 | 3.1 | 4.3 | 15 | 15 | 15 |
| b3 (1+) | 6 | 2.7 | 2.2 | 7.1 | 3 | 3.3 | 9.3 | 4 | 4 | 15 | 15 | 15 |
| y6 (1+) | 7.2 | 4 | 3.8 | 7 | 4 | 4.1 | 10 | 5.7 | 5.6 | 15 | 15 | 15 |
| sum | 3.3 | 1.4 | 2 | 4.8 | 2.3 | 2.7 | 5.8 | 2.7 | 3.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5570 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
GYASPDLSK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
564
Peptide End
572
CPTAC ID
non-CPTAC-5570
Peptide Molecular Mass
936.4553
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Line
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
RSLCnano and Quantiva
Internal Standard
SIS Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
RSLCnano
Column Packing
C18 PepMap100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| b2 (1+) | 19 | 6.4 | 5 | 27.6 | 30 | 15.6 | 33.5 | 30.7 | 16.4 | 14 | 14 | 14 |
| y5 (1+) | 22.3 | 6.1 | 5.7 | 26.1 | 27 | 15.3 | 34.3 | 27.7 | 16.3 | 14 | 14 | 14 |
| y6 (1+) | 19.3 | 7.9 | 4.9 | 26 | 31 | 17 | 32.4 | 32 | 17.7 | 14 | 14 | 14 |
| y7 (1+) | 19 | 6.1 | 4.4 | 26.7 | 30.2 | 15.9 | 32.8 | 30.8 | 16.5 | 14 | 14 | 14 |
| sum | 18.6 | 6.2 | 4.7 | 25.6 | 29.8 | 15.9 | 31.6 | 30.4 | 16.6 | 14 | 14 | 14 |
Additional Resources and Comments
Assay Details for non-CPTAC-5432 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
STSTPNVHMVSTTLPVDSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
257
Peptide End
275
CPTAC ID
non-CPTAC-5432
Peptide Molecular Mass
2,027.9946
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Cell Lysate
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
RSLCnano and Quantiva
Internal Standard
Stable Isotope Labeled Standard
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y15 (2+) | 7.7 | 3.4 | 2.7 | 8.4 | 4.8 | 2.8 | 11.4 | 5.9 | 3.9 | 15 | 15 | 15 |
| y17 (2+) | 6 | 2.5 | 2.7 | 7.6 | 4.9 | 4.4 | 9.7 | 5.5 | 5.2 | 15 | 15 | 15 |
| y5 (1+) | 3.7 | 1.6 | 2.2 | 3.7 | 2.9 | 3.2 | 5.2 | 3.3 | 3.9 | 15 | 15 | 15 |
| y9 (1+) | 9.9 | 5 | 3.1 | 10.7 | 5.7 | 4.1 | 14.6 | 7.6 | 5.1 | 15 | 15 | 15 |
| sum | 3.2 | 1.1 | 1.6 | 3.6 | 3.1 | 2.8 | 4.8 | 3.3 | 3.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5734 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
STS[+79.966331]TPNVHMVSTTLPVDSR
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
257
Peptide End
275
CPTAC ID
non-CPTAC-5734
Peptide Molecular Mass
2,107.9609
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Lysate
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Thermo Quantiva
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex Ultimate 3000 RSLCnano
Column Packing
Pepmap 100
Column Dimensions
75um x 25cm
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 1.8 | 1 | 1.1 | 2.5 | 1.3 | 1.9 | 3.1 | 1.6 | 2.2 | 15 | 15 | 15 |
| y6 (1+) | 3.4 | 3.5 | 3.2 | 6.7 | 3.2 | 2.9 | 7.5 | 4.7 | 4.3 | 15 | 15 | 15 |
| y9 (1+) | 4.5 | 2.8 | 2.5 | 4.6 | 3.3 | 3 | 6.4 | 4.3 | 3.9 | 15 | 15 | 15 |
| y5 (2+) | 3.6 | 2.5 | 1.1 | 4.6 | 2.3 | 1.9 | 5.8 | 3.4 | 2.2 | 15 | 15 | 15 |
| y15 (2+) | 4.4 | 3.8 | 2.7 | 4.5 | 4.2 | 2.6 | 6.3 | 5.7 | 3.7 | 15 | 15 | 15 |
| sum | 1.3 | 0.5 | 0.7 | 2.3 | 0.6 | 1.2 | 2.6 | 0.8 | 1.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5569 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
VVDPTPEQFQAFR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
379
Peptide End
391
CPTAC ID
non-CPTAC-5569
Peptide Molecular Mass
1,532.7623
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
Fe(III)-NTA
Matrix
Cell Line
Submitting Laboratory
Moffitt Cancer Center
Submitting Lab PI
John Koomen
Publication
View Details (opens in a new window)
Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Cell Reports Methods doi: 10.1016/j.crmeth.2021.100015.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
RSLCnano and Quantiva
Internal Standard
SIS Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
RSLCnano
Column Packing
C18 PepMap100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y6 (1+) | 18.7 | 10.1 | 12 | 24.3 | 33.5 | 15.6 | 30.7 | 35 | 19.7 | 14 | 14 | 14 |
| y8 (1+) | 20.5 | 9.5 | 12.4 | 27.6 | 33.3 | 15.6 | 34.4 | 34.6 | 19.9 | 14 | 14 | 14 |
| y10 (1+) | 27.6 | 8.6 | 11.9 | 27.8 | 35.2 | 15.8 | 39.2 | 36.2 | 19.8 | 14 | 14 | 14 |
| y11 (1+) | 29 | 13.1 | 10.3 | 33.2 | 32.6 | 15.7 | 44.1 | 35.1 | 18.8 | 14 | 14 | 14 |
| sum | 21.3 | 9.5 | 12 | 27 | 33.6 | 15.6 | 34.4 | 34.9 | 19.7 | 14 | 14 | 14 |
Additional Resources and Comments
Assay Details for CPTAC-1762 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Modified Sequence
LVADC[+57.0]VK
Modification Type
Carbamidomethyl (C)
Protein - Site of Modification
588
Peptide - Site of Modification
5
Peptide Start
584
Peptide End
590
CPTAC ID
CPTAC-1762
Peptide Molecular Mass
803.4211
Species
Homo sapiens (Human)
Assay Type
Fractionation MRM
Fractionation Approach
N/A
Matrix
Ovarian cancer tumor tissue lysate
Submitting Laboratory
Pacific Northwest National Laboratory
Submitting Lab PI
Tao Liu
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Waters nanoACQUITY (Part Number 176016000)
Column Packing
Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions
100 um x 100 mm
Flow Rate
0.4 (uL/min)
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y3 (1+) | 26.8 | 4.6 | 3.5 | 35.6 | 6.7 | 3.8 | 44.6 | 8.1 | 5.2 | 15 | 15 | 15 |
| y5 (1+) | 6.6 | 4.5 | 1.8 | 6.7 | 4.8 | 1.9 | 9.4 | 6.6 | 2.6 | 15 | 15 | 15 |
| y6 (1+) | 19.8 | 14.5 | 1.6 | 24.6 | 18.7 | 5.7 | 31.6 | 23.7 | 5.9 | 15 | 15 | 15 |
| sum | 6.5 | 2.8 | 1.2 | 7.3 | 4.7 | 2.1 | 9.8 | 5.5 | 2.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1546 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAF1
Peptide Sequence
TISNGFGFK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
10
Peptide End
18
CPTAC ID
CPTAC-1546
Peptide Molecular Mass
969.4920
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Ovarian cancer tumor tissue lysate
Submitting Laboratory
Pacific Northwest National Laboratory
Submitting Lab PI
Tao Liu
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Waters nanoACQUITY (Part Number 176016000)
Column Packing
Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions
100 um x 100 mm
Flow Rate
0.5 uL/min
Assay Multiplexing Expand assay panel
Broad Institute-Biologist curated set of targets across a number of important cancer pathways
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y7 (1+) | 11.9 | 3.4 | 2.4 | 15.2 | 4.8 | 6.6 | 19.3 | 5.9 | 7 | 15 | 15 | 15 |
| y5 (1+) | 39 | 6.4 | 5 | 55.8 | 7.6 | 8.2 | 68.1 | 9.9 | 9.6 | 15 | 15 | 15 |
| y3 (1+) | 29.2 | 5.2 | 6.5 | 21.8 | 4.3 | 9.8 | 36.4 | 6.7 | 11.8 | 15 | 15 | 15 |
| b2 (1+) | 9.7 | 3.5 | 3.1 | 10.6 | 5.6 | 6.4 | 14.4 | 6.6 | 7.1 | 15 | 15 | 15 |
| sum | 6 | 2.8 | 2.1 | 10.4 | 4.7 | 6.2 | 12 | 5.5 | 6.5 | 15 | 15 | 15 |