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Please include the following statement when referencing the CPTAC Assay Portal
We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.

PTPRC

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PTPRC CD45
Sequence Length (AA) Molecular Weight (Da)
1306 147486
Protein Name
Receptor-type tyrosine-protein phosphatase C
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MTMYLWLKLL AFGFAFLDTE VFVTGQSPTP SPTGLTTAKM PSVPLSSDPL
60 70 80 90 100
PTHTTAFSPA STFERENDFS ETTTSLSPDN TSTQVSPDSL DNASAFNTTG
110 120 130 140 150
VSSVQTPHLP THADSQTPSA GTDTQTFSGS AANAKLNPTP GSNAISDVPG
160 170 180 190 200
ERSTASTFPT DPVSPLTTTL SLAHHSSAAL PARTSNTTIT ANTSDAYLNA
210 220 230 240 250
SETTTLSPSG SAVISTTTIA TTPSKPTCDE KYANITVDYL YNKETKLFTA
260 270 280 290 300
KLNVNENVEC GNNTCTNNEV HNLTECKNAS VSISHNSCTA PDKTLILDVP
310 320 330 340 350
PGVEKFQLHD CTQVEKADTT ICLKWKNIET FTCDTQNITY RFQCGNMIFD
360 370 380 390 400
NKEIKLENLE PEHEYKCDSE ILYNNHKFTN ASKIIKTDFG SPGEPQIIFC
410 420 430 440 450
RSEAAHQGVI TWNPPQRSFH NFTLCYIKET EKDCLNLDKN LIKYDLQNLK
460 470 480 490 500
PYTKYVLSLH AYIIAKVQRN GSAAMCHFTT KSAPPSQVWN MTVSMTSDNS
510 520 530 540 550
MHVKCRPPRD RNGPHERYHL EVEAGNTLVR NESHKNCDFR VKDLQYSTDY
560 570 580 590 600
TFKAYFHNGD YPGEPFILHH STSYNSKALI AFLAFLIIVT SIALLVVLYK
610 620 630 640 650
IYDLHKKRSC NLDEQQELVE RDDEKQLMNV EPIHADILLE TYKRKIADEG
660 670 680 690 700
RLFLAEFQSI PRVFSKFPIK EARKPFNQNK NRYVDILPYD YNRVELSEIN
710 720 730 740 750
GDAGSNYINA SYIDGFKEPR KYIAAQGPRD ETVDDFWRMI WEQKATVIVM
760 770 780 790 800
VTRCEEGNRN KCAEYWPSME EGTRAFGDVV VKINQHKRCP DYIIQKLNIV
810 820 830 840 850
NKKEKATGRE VTHIQFTSWP DHGVPEDPHL LLKLRRRVNA FSNFFSGPIV
860 870 880 890 900
VHCSAGVGRT GTYIGIDAML EGLEAENKVD VYGYVVKLRR QRCLMVQVEA
910 920 930 940 950
QYILIHQALV EYNQFGETEV NLSELHPYLH NMKKRDPPSE PSPLEAEFQR
960 970 980 990 1000
LPSYRSWRTQ HIGNQEENKS KNRNSNVIPY DYNRVPLKHE LEMSKESEHD
1010 1020 1030 1040 1050
SDESSDDDSD SEEPSKYINA SFIMSYWKPE VMIAAQGPLK ETIGDFWQMI
1060 1070 1080 1090 1100
FQRKVKVIVM LTELKHGDQE ICAQYWGEGK QTYGDIEVDL KDTDKSSTYT
1110 1120 1130 1140 1150
LRVFELRHSK RKDSRTVYQY QYTNWSVEQL PAEPKELISM IQVVKQKLPQ
1160 1170 1180 1190 1200
KNSSEGNKHH KSTPLLIHCR DGSQQTGIFC ALLNLLESAE TEEVVDIFQV
1210 1220 1230 1240 1250
VKALRKARPG MVSTFEQYQF LYDVIASTYP AQNGQVKKNN HQEDKIEFDN
1260 1270 1280 1290 1300
EVDKVKQDAN CVNPLGAPEK LPEAKEQAEG SEPTSGTEGP EHSVNGPASP
1306
ALNQGS

Data source: UniProt

Protein Map Collapse protein map

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

Uniprot Database Entry PhosphoSitePlus ®

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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-5846 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
DPPSEPSPLEAEFQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
936
Peptide End
950
CPTAC ID
CPTAC-5846
Peptide Molecular Mass
1,697.7897
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
Frozen breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  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+) 27.1 13.9 10 26.9 15.2 14.3 38.2 20.6 17.4 15 17 15
y10 (1+) 17.6 9.4 6.7 21.5 8.4 10.2 27.8 12.6 12.2 15 17 15
y13 (1+) 31.7 11.1 8.1 32.3 13.3 11.4 45.3 17.3 14 15 17 15
y13 (2+) 19.6 11.9 9.7 22.5 11.4 9.6 29.8 16.5 13.6 15 17 15
y14 (2+) 25.7 12.8 6.1 27.8 13.1 9.2 37.9 18.3 11 15 17 15
sum 14.1 8.7 4.7 15.8 8.2 8.8 21.2 12 10 15 17 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-5871 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
DPPSEPSPLEAEFQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
936
Peptide End
950
CPTAC ID
CPTAC-5871
Peptide Molecular Mass
1,697.7897
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Chromatograms

Data source: Panorama

view larger image
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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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
y13 (2+) 25.6 11.9 6.9 29.2 14.2 10.7 38.8 18.5 12.7 12 12 12
y14 (2+) 28.4 15.2 10.5 22.6 15.4 8 36.3 21.6 13.2 12 12 12
y8 (1+) 43.8 25.1 13.7 49.4 13.9 12.4 66 28.7 18.5 12 12 12
y10 (1+) 21.2 7.8 7.5 25.8 7.1 7.1 33.4 10.5 10.3 12 12 12
y13 (1+) 43.7 10.2 14.7 41 19.9 13.7 59.9 22.4 20.1 12 12 12
sum 21 8.2 4.8 20.4 6.8 5.2 29.3 10.7 7.1 12 12 12

Additional Resources and Comments

Resources
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Comments

Assay Details for CPTAC-5946 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
DPPSEPSPLEAEFQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
936
Peptide End
950
CPTAC ID
CPTAC-5946
Peptide Molecular Mass
1,697.7897
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 µL/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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+) 5.5 7.6 7.2 8.7 12.8 16.3 10.3 14.9 17.8 13 25 14
y8 (1+) 10.3 7.5 9.7 10.6 11.4 9.7 14.8 13.6 13.7 13 25 14
y14 (2+) 13.4 5.9 5 18.1 8 12 22.5 9.9 13 13 25 14
y13 (2+) 12.9 6.3 5.8 17 8.6 7.9 21.3 10.7 9.8 13 25 14
sum 5.6 6 4.8 10.2 10 12.4 11.6 11.7 13.3 13 25 14

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-5847 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
LFLAEFQSIPR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
652
Peptide End
662
CPTAC ID
CPTAC-5847
Peptide Molecular Mass
1,319.7238
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
Frozen breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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+) 17.3 10.3 11.9 17.6 18.5 19.6 24.7 21.2 22.9 15 17 15
y6 (1+) 12.6 9.5 11.1 15.6 19.7 19.6 20.1 21.9 22.5 15 17 15
y7 (1+) 6.5 12.9 13.2 15.2 21.1 22.3 16.5 24.7 25.9 15 17 15
y8 (1+) 10.9 9.8 11.1 14.8 17.3 20.8 18.4 19.9 23.6 15 17 15
y9 (1+) 8.6 10.4 11.2 15 20.1 21.5 17.3 22.6 24.2 15 17 15
sum 8.6 9.7 10.7 13.4 18.8 20.6 15.9 21.2 23.2 15 17 15

Additional Resources and Comments

Resources
Download SOPs
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Comments

Assay Details for CPTAC-5872 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
LFLAEFQSIPR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
6
Peptide Start
652
Peptide End
662
CPTAC ID
CPTAC-5872
Peptide Molecular Mass
1,319.7238
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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+) 10.6 4.7 8.8 15.1 10.7 9.3 18.4 11.7 12.8 12 12 12
y5 (1+) 19.1 5.4 6.6 19.3 7 5.5 27.2 8.8 8.6 12 12 12
y7 (1+) 18 11.8 10.2 19 10.1 9.3 26.2 15.5 13.8 12 12 12
y8 (1+) 13.6 6.8 9.5 16.2 7 8.8 21.2 9.8 12.9 12 12 12
y9 (1+) 12.9 8.1 9.1 12.2 11.5 9.5 17.8 14.1 13.2 12 12 12
sum 12.1 6.8 8.3 14.5 8.8 8.6 18.9 11.1 12 12 12 12

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments

Assay Details for CPTAC-5945 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
LFLAEFQSIPR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
652
Peptide End
662
CPTAC ID
CPTAC-5945
Peptide Molecular Mass
1,319.7238
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 µL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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+) 6.8 5.7 2.9 14.3 11.4 9.8 15.8 12.7 10.2 13 25 14
y9 (1+) 7.1 4.8 4 17.5 9.6 11.1 18.9 10.7 11.8 13 25 14
y8 (1+) 8.5 5.3 3.5 17.2 10.1 9.4 19.2 11.4 10 13 25 14
y7 (1+) 8 4.5 4.1 14.5 10.1 10.4 16.6 11.1 11.2 13 25 14
y5 (1+) 7.6 4.9 3.6 15.4 10.6 10.6 17.2 11.7 11.2 13 25 14
sum 7.3 4.6 3.2 15.7 10 9.9 17.3 11 10.4 13 25 14

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-1172 Collapse assay details

Data source: Panorama

Official Gene Symbol
PTPRC
Peptide Sequence
LFLAEFQSIPR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
652
Peptide End
662
CPTAC ID
CPTAC-1172
Peptide Molecular Mass
1,319.7238
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

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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+) 12.9 9.9 4.9 18.2 9.2 7.7 22.3 13.5 9.1 15 15 15
y8 (1+) 13.9 7.4 6.6 13.5 7.3 7.4 19.4 10.4 9.9 15 15 15
y9 (1+) 15.5 6.8 7.2 20.2 7.9 8.5 25.5 10.4 11.1 15 15 15
sum 9.6 4.2 3.4 9.9 6.6 4.6 13.8 7.8 5.7 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments