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Overview Data source: UniProt

Official Gene Symbol Other Aliases
RAF1 RAF
Sequence Length (AA) Molecular Weight (Da)
648 73052
Protein Name
RAF proto-oncogene serine/threonine-protein kinase
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

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 ®

Click a point on a node
to view detailed assay information below
All other points link out to UniProt



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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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

Loader

Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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


Additional Resources and Comments