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Overview Data source: UniProt

Official Gene Symbol Other Aliases
BRAF BRAF1, RAFB1
Sequence Length (AA) Molecular Weight (Da)
766 84437
Protein Name
Serine/threonine-protein kinase B-raf
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI
60 70 80 90 100
KQMIKLTQEH IEALLDKFGG EHNPPSIYLE AYEEYTSKLD ALQQREQQLL
110 120 130 140 150
ESLGNGTDFS VSSSASMDTV TSSSSSSLSV LPSSLSVFQN PTDVARSNPK
160 170 180 190 200
SPQKPIVRVF LPNKQRTVVP ARCGVTVRDS LKKALMMRGL IPECCAVYRI
210 220 230 240 250
QDGEKKPIGW DTDISWLTGE ELHVEVLENV PLTTHNFVRK TFFTLAFCDF
260 270 280 290 300
CRKLLFQGFR CQTCGYKFHQ RCSTEVPLMC VNYDQLDLLF VSKFFEHHPI
310 320 330 340 350
PQEEASLAET ALTSGSSPSA PASDSIGPQI LTSPSPSKSI PIPQPFRPAD
360 370 380 390 400
EDHRNQFGQR DRSSSAPNVH INTIEPVNID DLIRDQGFRG DGGSTTGLSA
410 420 430 440 450
TPPASLPGSL TNVKALQKSP GPQRERKSSS SSEDRNRMKT LGRRDSSDDW
460 470 480 490 500
EIPDGQITVG QRIGSGSFGT VYKGKWHGDV AVKMLNVTAP TPQQLQAFKN
510 520 530 540 550
EVGVLRKTRH VNILLFMGYS TKPQLAIVTQ WCEGSSLYHH LHIIETKFEM
560 570 580 590 600
IKLIDIARQT AQGMDYLHAK SIIHRDLKSN NIFLHEDLTV KIGDFGLATV
610 620 630 640 650
KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM
660 670 680 690 700
TGQLPYSNIN NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK
710 720 730 740 750
RDERPLFPQI LASIELLARS LPKIHRSASE PSLNRAGFQT EDFSLYACAS
760 766
PKTPIQAGGY GAFPVH

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-5817 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
DS[+79.966331]SDDWEIPDGQITVGQR
Modification Type
Phospho (S,T)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
445
Peptide End
462
CPTAC ID
CPTAC-5817
Peptide Molecular Mass
2,096.8688
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y10 (2+) 35.7 15.4 35.1 34.8 24 43.9 49.9 28.5 56.2 16 15 16
b8-98 (1+) 64.3 33.6 16.9 103.4 38.1 34.5 121.8 50.8 38.4 16 15 15
sum 39.5 16.8 33.9 42.3 23.9 44.1 57.9 29.2 55.6 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5818 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
DSSDDWEIPDGQITVGQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
445
Peptide End
462
CPTAC ID
CPTAC-5818
Peptide Molecular Mass
2,016.9025
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y10 (2+) 23.5 10.5 6 29.3 14.9 13.9 37.6 18.2 15.1 16 15 17
y6 (1+) 46 9.3 23.5 49.5 19.1 22.9 67.6 21.2 32.8 16 15 17
sum 24 9 19 27.9 14.4 17.6 36.8 17 25.9 16 15 17


Additional Resources and Comments


Assay Details for CPTAC-5821 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
GDGGSTTGLSATPPASLPGSLTNVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
390
Peptide End
414
CPTAC ID
CPTAC-5821
Peptide Molecular Mass
2,284.1547
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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 K
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min

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
b12 (1+) 20.1 8.4 6.8 19.5 8.8 7.2 28 12.2 9.9 16 15 17
y8 (1+) 13.9 6.5 7.3 11.1 6.9 7.3 17.8 9.5 10.3 16 15 17
sum 12.5 6.6 6.9 9.6 7 7.1 15.8 9.6 9.9 16 15 17


Additional Resources and Comments


Assay Details for CPTAC-5822 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
GDGGSTTGLSAT[+79.966331]PPASLPGSLTNVK
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
390
Peptide End
414
CPTAC ID
CPTAC-5822
Peptide Molecular Mass
2,364.1210
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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 K
LC
Dionex Ultimate 3000
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nL/min

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+) 11.7 11.3 17.2 15.3 18.2 21.1 19.3 21.4 27.2 16 15 16
y13 (2+) 14.9 11.1 27.3 16.5 16.7 34 22.2 20.1 43.6 16 15 16
y8 (2+) 10.5 9 9.5 17.7 16.8 20.6 20.6 19.1 22.7 16 15 16
sum 10.9 10.2 13.2 15.7 17.4 21.6 19.1 20.2 25.3 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5771 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
GLIPEC[+57.021464]C[+57.021464]AVYR
Modification Type
Carbamidomethyl (C)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
189
Peptide End
199
CPTAC ID
CPTAC-5771
Peptide Molecular Mass
1,336.6268
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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+) 22.6 13.1 7.4 18.8 31.7 18.7 29.4 34.3 20.1 15 15 15
y7 (1+) 25.8 10.4 8.2 34.1 30.8 18.3 42.8 32.5 20.1 15 15 15
y8 (1+) 19.8 11 7.9 26.4 31.9 18 33 33.7 19.7 15 15 15
sum 19.5 11.3 7.6 24 31.7 18.1 30.9 33.7 19.6 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-5819 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
RDS[+79.966331]SDDWEIPDGQITVGQR
Modification Type
Phospho (S,T)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
444
Peptide End
462
CPTAC ID
CPTAC-5819
Peptide Molecular Mass
2,252.9699
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y9 (1+) 20.6 7.5 23.5 24.4 27.6 34.4 31.9 28.6 41.7 16 15 16
y11 (2+) 24.1 6 19.1 29.9 21.3 33.6 38.4 22.1 38.6 16 15 16
sum 9.3 5.9 18.8 17 23.3 33.4 19.4 24 38.3 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5820 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
RDSSDDWEIPDGQITVGQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
444
Peptide End
462
CPTAC ID
CPTAC-5820
Peptide Molecular Mass
2,173.0036
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y10 (1+) 9.8 10.3 6.8 14.7 15.5 11.8 17.7 18.6 13.6 16 15 17
b8 (1+) 7.9 11.7 5.9 16.4 16.7 12.1 18.2 20.4 13.5 16 15 17
sum 7.8 9.9 6.1 14.3 16 11.8 16.3 18.8 13.3 16 15 17


Additional Resources and Comments


Assay Details for non-CPTAC-5357 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
AGFQTEDFSLYAC[+57.021464]ASPK
Modification Type
Carbamidomethyl (C)
Protein - Site of Modification
749
Peptide - Site of Modification
13
Peptide Start
736
Peptide End
752
CPTAC ID
non-CPTAC-5357
Peptide Molecular Mass
1,890.8458
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 K
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min

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
y9 (1+) 14 5 2.2 14.3 6 4.3 20 7.8 4.8 15 15 15
y11 (1+) 17.5 5.2 3.5 17.2 5.5 4.9 24.5 7.6 6 15 15 15
y13 (1+) 16.8 5.4 3.3 16.5 8.6 3.7 23.5 10.2 5 15 15 15
y6 (1+) 12.5 5.2 4.1 18.4 6 4 22.2 7.9 5.7 15 15 15
y7 (1+) 11.4 5 4.5 13.1 8.8 4.1 17.4 10.1 6.1 15 15 15
sum 3.2 1.6 1.6 4.6 3.5 2.8 5.6 3.8 3.2 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5355 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
DSSDDWEIPDGQITVGQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
445
Peptide End
462
CPTAC ID
non-CPTAC-5355
Peptide Molecular Mass
2,016.9025
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

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
b8 (1+) 6.9 2.3 3.3 10.9 3.8 3.7 12.9 4.4 5 15 15 15
b7 (1+) 13.9 3.2 3.8 14.8 4.5 3.8 20.3 5.5 5.4 15 15 15
y3 (1+) 13.3 3.7 1.5 12.6 4.5 1.9 18.3 5.8 2.4 15 15 15
y10 (1+) 4.8 2.1 1.1 4.9 3.5 2.9 6.9 4.1 3.1 15 15 15
sum 4 1.4 0.9 5.1 2.9 2.1 6.5 3.2 2.3 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5727 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
DS[+79.966331]SDDWEIPDGQITVGQR
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
445
Peptide End
462
CPTAC ID
non-CPTAC-5727
Peptide Molecular Mass
2,096.8688
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y10 (1+) 5 3.6 2.8 5.9 3.9 2.9 7.7 5.3 4 14 15 15
y8 (1+) 9.5 7.7 3.4 10.2 4.4 5.1 13.9 8.9 6.1 14 15 15
y5 (1+) 13.6 11.3 8 18.4 10.3 6.7 22.9 15.3 10.4 14 15 15
b7-98 (1+) 10 5.1 5.8 12.3 6.3 4.2 15.9 8.1 7.2 14 15 15
y11 (1+) 12.3 8.1 4.4 13.2 9.5 6 18 12.5 7.4 14 15 15
sum 3.3 2.8 1.9 5.1 2.6 1.9 6.1 3.8 2.7 14 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5353 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
GDGGSTTGLSATPPASLPGSLTNVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
390
Peptide End
414
CPTAC ID
non-CPTAC-5353
Peptide Molecular Mass
2,284.1547
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 K
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min

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
b12 (1+) 18.2 16.1 43.9 27.7 14 80.9 33.1 21.3 92 15 15 15
y8 (1+) 11.4 6 4.8 18.8 6.9 4.7 22 9.1 6.7 15 15 15
sum 9.2 6.1 4.7 17.6 6.6 4.9 19.9 9 6.8 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5729 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
GDGGSTTGLSAT[+79.966331]PPASLPGSLTNVK
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
390
Peptide End
414
CPTAC ID
non-CPTAC-5729
Peptide Molecular Mass
2,364.1210
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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 K
LC
Dionex Ultimate 3000 RSLCnano
Column Packing
Pepmap 100
Column Dimensions
75um x 25cm
Flow Rate
300 nL/min

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 (2+) 4.3 1.7 2.3 4.4 3.4 2.9 6.2 3.8 3.7 15 15 15
y13 (2+) 8.5 5.8 5.9 10.2 6.3 6.5 13.3 8.6 8.8 15 15 15
y8 (1+) 2.1 2.8 2.5 3.7 3 3.4 4.3 4.1 4.2 15 15 15
sum 2.2 2.4 2.2 3.6 3 3.1 4.2 3.8 3.8 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5352 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
GLIPEC[+57.021464]C[+57.021464]AVYR
Modification Type
Carbamidomethyl (C), Carbamidomethyl (C)
Protein - Site of Modification
195, 196
Peptide - Site of Modification
6, 7
Peptide Start
189
Peptide End
199
CPTAC ID
non-CPTAC-5352
Peptide Molecular Mass
1,336.6268
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

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+) 12.3 5.7 5.3 12.9 6.1 5.7 17.8 8.3 7.8 15 15 15
y6 (1+) 8.5 3.8 2.7 8.5 3.6 3.1 12 5.2 4.1 15 15 15
y7 (1+) 8.4 5.9 2.8 10.6 6.4 2.6 13.5 8.7 3.8 15 15 15
y8 (1+) 11.2 1.3 2.5 15.9 3 3.1 19.4 3.3 4 15 15 15
sum 9.1 1.2 1.7 12.6 2.5 2.3 15.5 2.8 2.9 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5354 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
RDSSDDWEIPDGQITVGQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
444
Peptide End
462
CPTAC ID
non-CPTAC-5354
Peptide Molecular Mass
2,173.0036
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

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
b8 (1+) 7.5 3.4 2.1 9.4 2.7 4.4 12 4.3 4.9 15 15 15
y3 (1+) 10.9 5.9 3.9 12.1 5.4 4.8 16.3 8 6.2 15 15 15
y8 (1+) 16.8 3.5 4 16.5 7.5 4 23.5 8.3 5.7 15 15 15
y10 (1+) 5.7 3.5 2.8 7.5 3.1 3 9.4 4.7 4.1 15 15 15
sum 4.7 3.2 1.6 5.7 2.7 2.9 7.4 4.2 3.3 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5728 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Modified Sequence
RDS[+79.966331]SDDWEIPDGQITVGQR
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
444
Peptide End
462
CPTAC ID
non-CPTAC-5728
Peptide Molecular Mass
2,252.9699
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
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

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
y10 (2+) 3.9 2.3 4.6 8 7.2 8.7 8.9 7.6 9.8 15 15 15
y5 (1+) 12 5.4 4.3 17.2 9.9 9.2 21 11.3 10.2 15 15 15
y8 (1+) 18.5 10.6 8.4 30.1 23.3 22 35.3 25.6 23.5 15 15 15
y10 (1+) 6.7 3.1 4.3 10.2 8 9.6 12.2 8.6 10.5 15 15 15
sum 4.1 2.2 3.7 8.4 8.1 9.5 9.3 8.4 10.2 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5356 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRAF
Peptide Sequence
SNNIFLHEDLTVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
579
Peptide End
591
CPTAC ID
non-CPTAC-5356
Peptide Molecular Mass
1,528.7886
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 K
LC
RSLCnano
Column Packing
C18 PepMap 100
Column Dimensions
75 micron ID x 25 cm length
Flow Rate
300 nl/min

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+) 30.9 9.4 5.2 29.1 9.5 5.9 42.4 13.4 7.9 15 15 15
y6 (1+) 22.5 7.3 3.2 18.8 8.2 4.7 29.3 11 5.7 15 15 15
y7 (1+) 10.8 3.5 4.2 12.8 5.7 4 16.7 6.7 5.8 15 15 15
sum 10.5 3.8 2.6 8.1 4.3 3.5 13.3 5.7 4.4 15 15 15


Additional Resources and Comments