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Overview Data source: UniProt

Official Gene Symbol Other Aliases
Egfr N/A
Sequence Length (AA) Molecular Weight (Da)
1210 134853
Protein Name
Epidermal growth factor receptor
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MRPSGTARTT LLVLLTALCA AGGALEEKKV CQGTSNRLTQ LGTFEDHFLS
60 70 80 90 100
LQRMYNNCEV VLGNLEITYV QRNYDLSFLK TIQEVAGYVL IALNTVERIP
110 120 130 140 150
LENLQIIRGN ALYENTYALA ILSNYGTNRT GLRELPMRNL QEILIGAVRF
160 170 180 190 200
SNNPILCNMD TIQWRDIVQN VFMSNMSMDL QSHPSSCPKC DPSCPNGSCW
210 220 230 240 250
GGGEENCQKL TKIICAQQCS HRCRGRSPSD CCHNQCAAGC TGPRESDCLV
260 270 280 290 300
CQKFQDEATC KDTCPPLMLY NPTTYQMDVN PEGKYSFGAT CVKKCPRNYV
310 320 330 340 350
VTDHGSCVRA CGPDYYEVEE DGIRKCKKCD GPCRKVCNGI GIGEFKDTLS
360 370 380 390 400
INATNIKHFK YCTAISGDLH ILPVAFKGDS FTRTPPLDPR ELEILKTVKE
410 420 430 440 450
ITGFLLIQAW PDNWTDLHAF ENLEIIRGRT KQHGQFSLAV VGLNITSLGL
460 470 480 490 500
RSLKEISDGD VIISGNRNLC YANTINWKKL FGTPNQKTKI MNNRAEKDCK
510 520 530 540 550
AVNHVCNPLC SSEGCWGPEP RDCVSCQNVS RGRECVEKCN ILEGEPREFV
560 570 580 590 600
ENSECIQCHP ECLPQAMNIT CTGRGPDNCI QCAHYIDGPH CVKTCPAGIM
610 620 630 640 650
GENNTLVWKY ADANNVCHLC HANCTYGCAG PGLQGCEVWP SGPKIPSIAT
660 670 680 690 700
GIVGGLLFIV VVALGIGLFM RRRHIVRKRT LRRLLQEREL VEPLTPSGEA
710 720 730 740 750
PNQAHLRILK ETEFKKIKVL GSGAFGTVYK GLWIPEGEKV KIPVAIKELR
760 770 780 790 800
EATSPKANKE ILDEAYVMAS VDNPHVCRLL GICLTSTVQL ITQLMPYGCL
810 820 830 840 850
LDYVREHKDN IGSQYLLNWC VQIAKGMNYL EDRRLVHRDL AARNVLVKTP
860 870 880 890 900
QHVKITDFGL AKLLGAEEKE YHAEGGKVPI KWMALESILH RIYTHQSDVW
910 920 930 940 950
SYGVTVWELM TFGSKPYDGI PASDISSILE KGERLPQPPI CTIDVYMIMV
960 970 980 990 1000
KCWMIDADSR PKFRELILEF SKMARDPQRY LVIQGDERMH LPSPTDSNFY
1010 1020 1030 1040 1050
RALMDEEDME DVVDADEYLI PQQGFFNSPS TSRTPLLSSL SATSNNSTVA
1060 1070 1080 1090 1100
CINRNGSCRV KEDAFLQRYS SDPTGAVTED NIDDAFLPVP EYVNQSVPKR
1110 1120 1130 1140 1150
PAGSVQNPVY HNQPLHPAPG RDLHYQNPHS NAVGNPEYLN TAQPTCLSSG
1160 1170 1180 1190 1200
FNSPALWIQK GSHQMSLDNP DYQQDFFPKE TKPNGIFKGP TAENAEYLRV
1210
APPSSEFIGA

Data source: UniProt


Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

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to view detailed assay information below
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Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-5832 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
GSHQISLDNPDY[+79.966331]QQDFFPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1161
Peptide End
1179
CPTAC ID
CPTAC-5832
Peptide Molecular Mass
2,314.9896
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
b5 (1+) 11.6 11.6 10.2 9.6 14 11.3 15.1 18.2 15.2 16 15 16
b8 (1+) 12.2 10 5.5 13.9 14 8.2 18.5 17.2 9.9 16 15 16
b9 (1+) 10.3 11 8.2 12 14.1 9.7 15.8 17.9 12.7 16 15 16
sum 10 10.6 7.6 11.1 13.9 9.4 14.9 17.5 12.1 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5831 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
GSHQISLDNPDYQQDFFPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1161
Peptide End
1179
CPTAC ID
CPTAC-5831
Peptide Molecular Mass
2,235.0233
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y6 (1+) 11.3 5.3 4.6 12.6 10.3 5.1 16.9 11.6 6.9 16 15 17
b9 (1+) 9.8 5.7 4.9 12.2 12.7 5.1 15.6 13.9 7.1 16 15 17
sum 9 5.3 4.5 11.1 11.3 4.8 14.3 12.5 6.6 16 15 17


Additional Resources and Comments


Assay Details for CPTAC-5830 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
GSTAENAEY[+79.966331]LR
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1189
Peptide End
1199
CPTAC ID
CPTAC-5830
Peptide Molecular Mass
1,289.5289
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y5 (1+) 6.5 9.3 8.6 19.5 15.9 18.4 20.6 18.4 20.3 16 15 16
y6 (1+) 5.2 9.2 8.4 18.2 15.2 17.7 18.9 17.8 19.6 16 15 16
sum 5.6 9.2 8.4 18.7 15.5 18 19.5 18 19.9 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5785 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
IPLENLQIIR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
99
Peptide End
108
CPTAC ID
CPTAC-5785
Peptide Molecular Mass
1,207.7289
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y7 (1+) 19.7 14.8 7.7 20.1 31.8 14.8 28.1 35.1 16.7 15 15 15
y8 (1+) 31.8 16.8 10.8 41.1 33.6 14.8 52 37.6 18.3 15 15 15
sum 20.6 15.4 8.9 23.8 32.4 14.7 31.5 35.9 17.2 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-5784 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
NLQEILHGAVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
139
Peptide End
149
CPTAC ID
CPTAC-5784
Peptide Molecular Mass
1,248.6939
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y5 (1+) 47.7 20.4 8 47.5 33.6 17.7 67.3 39.3 19.4 15 15 15
y6 (1+) 29.9 10.1 8 36.7 34.5 18.8 47.3 35.9 20.4 15 15 15
y8 (1+) 32.1 18.1 9.1 34 32.6 21.1 46.8 37.3 23 15 15 15
sum 24.4 13.4 7.8 26.8 32.7 18.7 36.2 35.3 20.3 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-5835 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
Y[+79.966331]SSDPTGALTEDSIDDTFLPVPEYINQSVPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1069
Peptide End
1099
CPTAC ID
CPTAC-5835
Peptide Molecular Mass
3,477.5753
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
b9 (1+) 14.9 11 8.1 18.7 17.8 10.1 23.9 20.9 12.9 16 15 16
y10 (2+) 15.7 9.5 8.3 18.9 17.9 12 24.6 20.3 14.6 16 15 16
y10 (1+) 14.4 7.8 12.1 19.1 17.4 13.6 23.9 19.1 18.2 16 15 16
sum 14.5 8.5 7.3 18.4 17.5 10.3 23.4 19.5 12.6 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-5834 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
YSSDPTGALTEDSIDDTFLPVPEYINQSVPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1069
Peptide End
1099
CPTAC ID
CPTAC-5834
Peptide Molecular Mass
3,397.6089
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y10 (1+) 19.5 6.7 8.3 20.7 11.8 17 28.4 13.6 18.9 16 15 17
b8 (1+) 13.3 5.6 13.4 20.7 13.6 17.2 24.6 14.7 21.8 16 15 17
sum 16.6 6.1 8.8 19.3 11.8 16.8 25.5 13.3 19 16 15 17


Additional Resources and Comments


Assay Details for CPTAC-5833 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
YSSDPTGALTEDSIDDTFLPVPEY[+79.966331]INQSVPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1069
Peptide End
1099
CPTAC ID
CPTAC-5833
Peptide Molecular Mass
3,477.5753
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y12 (2+) 18.4 14.3 17.3 23.5 18.1 27.7 29.8 23.1 32.7 16 15 16
y10 (2+) 17.1 13 14.9 23.1 19.9 22.9 28.7 23.8 27.3 16 15 16
sum 15.9 12.2 14.9 22.1 18.9 20.1 27.2 22.5 25 16 15 16


Additional Resources and Comments


Assay Details for CPTAC-1781 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
VLGSGAFGTVY[+80.0]K
Modification Type
Phospho (Y)
Protein - Site of Modification
727
Peptide - Site of Modification
11
Peptide Start
717
Peptide End
728
CPTAC ID
CPTAC-1781
Peptide Molecular Mass
1,277.6057
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
E.coli lysate
Submitting Laboratory
Johns Hopkins University / Pandey
Submitting Lab PI
Akhilesh Pandey

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Orbitrap Fusion Lumos
Internal Standard
100fmol
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy nLC 1200 System
Column Packing
C18 2um 100A
Column Dimensions
75um i.d. x 50cm
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
y2 (1+) 9.1 5.4 5.6 11.8 8.5 6.2 14.9 10.1 8.4 15 15 15
y3 (1+) 42.6 10.9 12.7 37.2 10.6 13.7 56.6 15.2 18.7 15 15 15
y5 (1+) 12.1 6.7 6.8 14.1 7.6 6.6 18.6 10.1 9.5 15 15 15
y6 (1+) 7.7 6 6.9 10.2 7.5 7 12.8 9.6 9.8 15 15 15
y8 (1+) 19.9 8.5 6.1 20.6 9 10.2 28.6 12.4 11.9 15 15 15
y9 (1+) 19.5 10.2 10.4 31 9.5 9.7 36.6 13.9 14.2 15 15 15
y10 (1+) 9.5 5.5 6.4 8.4 7.2 6.1 12.7 9.1 8.8 15 15 15
sum 7.6 4 5.7 6.9 5.1 6 10.3 6.5 8.3 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5381 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
GSHQISLDNPDYQQDFFPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1161
Peptide End
1179
CPTAC ID
non-CPTAC-5381
Peptide Molecular Mass
2,235.0233
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
b9 (1+) 9.1 4 3.4 12.2 5 3.9 15.2 6.4 5.2 15 15 15
y10 (2+) 5 2.9 1.2 6.8 3.4 1.8 8.4 4.5 2.2 15 15 15
y3 (1+) 10.4 5.2 3.3 12.2 6.9 4 16 8.6 5.2 15 15 15
y6 (1+) 8.6 3.1 3.1 11.2 3.8 3.4 14.1 4.9 4.6 15 15 15
y7 (1+) 6.2 4.5 3.1 7.7 4.4 4.5 9.9 6.3 5.5 15 15 15
sum 3.3 2.5 1.2 3.8 3.6 1.7 5 4.4 2.1 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5737 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
GSHQISLDNPDY[+79.966331]QQDFFPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1161
Peptide End
1179
CPTAC ID
non-CPTAC-5737
Peptide Molecular Mass
2,314.9896
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y6 (1+) 3.3 4.7 3 3.8 4.3 3.9 5 6.4 4.9 15 15 15
b9 (1+) 4.4 1.9 1.8 4.6 2 3 6.4 2.8 3.5 15 15 15
b5 (1+) 10.6 3.4 2 11.8 5.5 3 15.9 6.5 3.6 15 15 15
b4 (1+) 6.3 2.1 2.9 8.3 2.4 3.6 10.4 3.2 4.6 15 15 15
y10 (2+) 1.9 1.3 1.4 1.9 1.4 1.7 2.7 1.9 2.2 15 15 15
sum 2.1 1.3 1.3 2.3 1.5 1.8 3.1 2 2.2 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5736 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
GSTAENAEY[+79.966331]LR
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1189
Peptide End
1199
CPTAC ID
non-CPTAC-5736
Peptide Molecular Mass
1,289.5289
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y8 (1+) 2.3 2.4 2.4 2.7 2.8 2.1 3.5 3.7 3.2 15 15 15
y4 (1+) 3 2.1 1.5 3.1 1.9 1.2 4.3 2.8 1.9 15 15 15
y5 (1+) 2.7 1.4 1.7 3.1 1.8 1.9 4.1 2.3 2.5 15 15 15
y6 (1+) 2.1 1.5 2.1 2.7 2.1 2.1 3.4 2.6 3 15 15 15
y7 (1+) 3.6 4 1.8 3.2 3.7 2.9 4.8 5.4 3.4 15 15 15
sum 1.6 1.1 1.4 2.2 1.4 1.2 2.7 1.8 1.8 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5382 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
GSTAENAEYLR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1189
Peptide End
1199
CPTAC ID
non-CPTAC-5382
Peptide Molecular Mass
1,209.5626
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
y4 (1+) 10.9 2.8 3 11 4 2.6 15.5 4.9 4 15 15 15
y8 (1+) 10.7 3.5 3.6 11.6 4 4.5 15.8 5.3 5.8 15 15 15
y6 (1+) 5.5 3.8 2.2 8 4.8 2.6 9.7 6.1 3.4 15 15 15
y7 (1+) 8.4 3.1 3 9.3 3 3.1 12.5 4.3 4.3 15 15 15
sum 5.1 2.2 1.8 6.3 2.6 2.1 8.1 3.4 2.8 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5545 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
IPLENLQIIR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
99
Peptide End
108
CPTAC ID
non-CPTAC-5545
Peptide Molecular Mass
1,207.7289
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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

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
y4 (1+) 29 9.2 10.3 38.2 34.8 16.7 48 36 19.6 14 14 14
y6 (1+) 34.6 12.5 8.2 40.4 30.6 14.8 53.2 33.1 16.9 14 14 14
y7 (1+) 17.5 13.1 7.9 21.2 32.3 14 27.5 34.9 16.1 14 14 14
y8 (1+) 18.3 15.2 10.6 30.9 33 12.9 35.9 36.3 16.7 14 14 14
y9 (1+) 45.6 15.1 9.8 59.2 21.2 14.8 74.7 26 17.8 14 14 14
sum 21.4 11.8 8.7 29.1 31.1 14.1 36.1 33.3 16.6 14 14 14


Additional Resources and Comments


Assay Details for non-CPTAC-5546 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
NLQEILHGAVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
139
Peptide End
149
CPTAC ID
non-CPTAC-5546
Peptide Molecular Mass
1,248.6939
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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

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+) 34.2 12.8 8.3 39.1 32.4 18.1 51.9 34.8 19.9 14 14 14
y6 (1+) 32.4 6.8 7.8 38.6 35.6 19.3 50.4 36.2 20.8 14 14 14
y8 (1+) 26.2 14.7 9 37.1 31.8 21.3 45.4 35 23.1 14 14 14
sum 25.8 8.5 8 28.4 32.5 19.1 38.4 33.6 20.7 14 14 14


Additional Resources and Comments


Assay Details for non-CPTAC-5738 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
Y[+79.966331]SSDPTGALTEDSIDDTFLPVPEYINQSVPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1069
Peptide End
1099
CPTAC ID
non-CPTAC-5738
Peptide Molecular Mass
3,477.5753
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y10 (2+) 1.9 1.7 1.7 3.4 2.8 3.4 3.9 3.3 3.8 15 15 15
y12 (2+) 2.9 1.9 2.2 2.5 2.2 3.2 3.8 2.9 3.9 15 15 15
y13 (2+) 3.7 2.7 2.3 4 2.6 3.1 5.4 3.7 3.9 15 15 15
y10 (1+) 2.8 2 1.2 3 2.7 2.7 4.1 3.4 3 15 15 15
y12 (1+) 1.5 1.6 1.5 3.5 2.6 3.6 3.8 3.1 3.9 15 15 15
sum 1.8 1.3 1.6 2.7 2.2 2.9 3.2 2.6 3.3 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5735 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
YSSDPTGALTEDSIDDTFLPVPEY[+79.966331]INQSVPK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
3
Peptide Start
1069
Peptide End
1099
CPTAC ID
non-CPTAC-5735
Peptide Molecular Mass
3,477.5753
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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
y12 (2+) 5 4.5 3.8 4.9 4 4.5 7 6 5.9 15 15 15
y13 (2+) 7.1 4.5 4.5 6 4.7 5.2 9.3 6.5 6.9 15 15 15
y10 (1+) 7.7 6.1 4.9 7.7 5.9 4.9 10.9 8.5 6.9 15 15 15
y12 (1+) 9.1 5.4 4.1 10.3 5.5 4.7 13.7 7.7 6.2 15 15 15
y10 (2+) 6.3 3.1 3.7 6.4 3.8 4 9 4.9 5.4 15 15 15
sum 4.9 3.6 3.7 5.2 3.8 4.2 7.1 5.2 5.6 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-5380 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
YSSDPTGALTEDSIDDTFLPVPEYINQSVPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1069
Peptide End
1099
CPTAC ID
non-CPTAC-5380
Peptide Molecular Mass
3,397.6089
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
y12 (1+) 13.8 3.8 2.7 17.2 13.4 7.3 22.1 13.9 7.8 15 15 15
y10 (2+) 10.1 3.8 4.7 16.3 13.5 8.1 19.2 14 9.4 15 15 15
y12 (2+) 10.3 4.1 3.3 20.8 14.8 7.2 23.2 15.4 7.9 15 15 15
y13 (2+) 11.9 3.7 5.6 18.3 11.4 7.4 21.8 12 9.3 15 15 15
y10 (1+) 9.4 4.8 3.4 21.6 13.7 7.2 23.6 14.5 8 15 15 15
sum 7.4 2 2.6 17.1 13.3 6.7 18.6 13.4 7.2 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-1560 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Sequence
LTQLGTFEDHFLSLQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
38
Peptide End
53
CPTAC ID
CPTAC-1560
Peptide Molecular Mass
1,903.9792
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 R
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

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+) 13.7 8 9.2 15.8 10.8 10 20.9 13.4 13.6 15 15 15
y6 (1+) 17.9 8.2 4.5 16.7 9.8 5.9 24.5 12.8 7.4 15 15 15
y13 (2+) 10.9 7 3.6 19.4 8.5 10 22.3 11 10.6 15 15 15
y12 (2+) 12.1 8 5.6 19.3 8.2 10.4 22.8 11.5 11.8 15 15 15
sum 8.3 6 3.5 17 7.3 9.3 18.9 9.4 9.9 15 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-3383 Collapse assay details

Data source: Panorama

Official Gene Symbol
Egfr
Peptide Sequence
IPLENLQIIR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
99
Peptide End
108
CPTAC ID
non-CPTAC-3383
Peptide Molecular Mass
1,207.7289
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers

Publication

View Details (opens in a new window)

Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Michaud SA, Sinclair NJ, Petrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y Eshghi A1, Richard VR, Sickmann A, Borchers CH. Commun Biol. 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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
b2 (1+) 4.7 4.4 3.8 11 6.9 4.8 12 8.2 6.1 15 15 15
y9 (2+) 4.7 5.5 2.6 15.1 9.5 3.9 15.8 11 4.7 15 15 15
y6 (1+) 2.5 3.8 3.1 13 6.5 4.6 13.2 7.5 5.5 15 15 15
y7 (1+) 3.8 3.4 4.7 16.6 6.3 4.7 17 7.2 6.6 15 15 15
y8 (1+) 3.4 3.2 2.8 13.6 10.6 6 14 11.1 6.6 15 15 15
sum 2.5 2.7 1.7 14.1 8 2.9 14.3 8.4 3.4 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-802 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
GSHQISLDNPDY[+80.0]QQDFFPK
Modification Type
Phospho (Y)
Protein - Site of Modification
1172
Peptide - Site of Modification
12
Peptide Start
1161
Peptide End
1179
CPTAC ID
CPTAC-802
Peptide Molecular Mass
2,314.9896
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Pooled patient derived xenograft breast tumor digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TripleTOF 5600+ (SCIEX)
Internal Standard
Peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
2DPlus nano-LC (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
200 µm x 15 cm
Flow Rate
800 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
y3 (1+) 35.3 17.3 12.2 28.3 18.2 12.9 45.2 25.1 17.8 15 15 15
y5 (1+) 28.5 18.3 17.1 31.4 21.9 27 42.4 28.5 32 15 15 15
y6 (1+) 39.5 27.2 21.2 48 34.6 21.5 62.2 44 30.2 15 15 15
b8 (1+) 37.4 22.2 17.4 40.5 22.2 20.5 55.1 31.4 26.9 15 15 15
b6 (1+) 40.5 16.6 13.2 45.5 21.9 21.3 60.9 27.5 25.1 15 15 15
b5 (1+) 23.2 11.6 18.3 24.2 15.9 15.9 33.5 19.7 24.2 15 15 15
b4 (1+) 28.5 8.3 11 31.7 9.2 11.3 42.6 12.4 15.8 15 15 15
b3 (1+) 35.8 12.9 7.5 37 13.9 9.5 51.5 19 12.1 15 15 15
sum 11.9 3.7 6.3 12.4 6.1 5.4 17.2 7.1 8.3 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-1043 Collapse assay details

Data source: Panorama

Official Gene Symbol
EGFR
Peptide Modified Sequence
MHLPSPTDSNFY[+80.0]R
Modification Type
Phospho (Y)
Protein - Site of Modification
998
Peptide - Site of Modification
12
Peptide Start
987
Peptide End
999
CPTAC ID
CPTAC-1043
Peptide Molecular Mass
1,643.6803
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Pooled patient derived xenograft breast tumor digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TripleTOF 5600+ (SCIEX)
Internal Standard
Peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
2DPlus nano-LC (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
200 µm x 15 cm
Flow Rate
800 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+) 24.7 15.9 9.1 29.1 13.3 8 38.2 20.7 12.1 15 15 15
y3 (1+) 23.3 14.6 10.1 27.6 13 10.7 36.1 19.5 14.7 15 15 15
b3 (1+) 18.5 10.3 5.9 17.4 7.5 7.6 25.4 12.7 9.6 15 15 15
sum 11.1 4.7 4.9 10.3 5 6.2 15.1 6.9 7.9 15 15 15


Additional Resources and Comments