CP, CPTAC-660 - CPTAC Assay Portal (original) (raw)
Please include the following statement when referencing the CPTAC Assay Portal
We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.
Protein Sequence hover to view complete sequence
non-CPTAC-3505: View additional DIFTGLIGPMK data
non-CPTAC-1093: View additional IYHSHIDAPK data
non-CPTAC-5587: View additional IYHSHVDAPK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MKILILGIFL | FLCSTPAWAK | EKHYYIGIIE | TTWDYASDHG | EKKLISVDTE |
| 60 | 70 | 80 | 90 | 100 |
| HSNIYLQNGP | DRIGRLYKKA | LYLQYTDETF | RTTIEKPVWL | GFLGPIIKAE |
| 110 | 120 | 130 | 140 | 150 |
| TGDKVYVHLK | NLASRPYTFH | SHGITYYKEH | EGAIYPDNTT | DFQRADDKVY |
| 160 | 170 | 180 | 190 | 200 |
| PGEQYTYMLL | ATEEQSPGEG | DGNCVTRIYH | SHIDAPKDIA | SGLIGPLIIC |
| 210 | 220 | 230 | 240 | 250 |
| KKDSLDKEKE | KHIDREFVVM | FSVVDENFSW | YLEDNIKTYC | SEPEKVDKDN |
| 260 | 270 | 280 | 290 | 300 |
| EDFQESNRMY | SVNGYTFGSL | PGLSMCAEDR | VKWYLFGMGN | EVDVHAAFFH |
| 310 | 320 | 330 | 340 | 350 |
| GQALTNKNYR | IDTINLFPAT | LFDAYMVAQN | PGEWMLSCQN | LNHLKAGLQA |
| 360 | 370 | 380 | 390 | 400 |
| FFQVQECNKS | SSKDNIRGKH | VRHYYIAAEE | IIWNYAPSGI | DIFTKENLTA |
| 410 | 420 | 430 | 440 | 450 |
| PGSDSAVFFE | QGTTRIGGSY | KKLVYREYTD | ASFTNRKERG | PEEEHLGILG |
| 460 | 470 | 480 | 490 | 500 |
| PVIWAEVGDT | IRVTFHNKGA | YPLSIEPIGV | RFNKNNEGTY | YSPNYNPQSR |
| 510 | 520 | 530 | 540 | 550 |
| SVPPSASHVA | PTETFTYEWT | VPKEVGPTNA | DPVCLAKMYY | SAVDPTKDIF |
| 560 | 570 | 580 | 590 | 600 |
| TGLIGPMKIC | KKGSLHANGR | QKDVDKEFYL | FPTVFDENES | LLLEDNIRMF |
| 610 | 620 | 630 | 640 | 650 |
| TTAPDQVDKE | DEDFQESNKM | HSMNGFMYGN | QPGLTMCKGD | SVVWYLFSAG |
| 660 | 670 | 680 | 690 | 700 |
| NEADVHGIYF | SGNTYLWRGE | RRDTANLFPQ | TSLTLHMWPD | TEGTFNVECL |
| 710 | 720 | 730 | 740 | 750 |
| TTDHYTGGMK | QKYTVNQCRR | QSEDSTFYLG | ERTYYIAAVE | VEWDYSPQRE |
| 760 | 770 | 780 | 790 | 800 |
| WEKELHHLQE | QNVSNAFLDK | GEFYIGSKYK | KVVYRQYTDS | TFRVPVERKA |
| 810 | 820 | 830 | 840 | 850 |
| EEEHLGILGP | QLHADVGDKV | KIIFKNMATR | PYSIHAHGVQ | TESSTVTPTL |
| 860 | 870 | 880 | 890 | 900 |
| PGETLTYVWK | IPERSGAGTE | DSACIPWAYY | STVDQVKDLY | SGLIGPLIVC |
| 910 | 920 | 930 | 940 | 950 |
| RRPYLKVFNP | RRKLEFALLF | LVFDENESWY | LDDNIKTYSD | HPEKVNKDDE |
| 960 | 970 | 980 | 990 | 1000 |
| EFIESNKMHA | INGRMFGNLQ | GLTMHVGDEV | NWYLMGMGNE | IDLHTVHFHG |
| 1010 | 1020 | 1030 | 1040 | 1050 |
| HSFQYKHRGV | YSSDVFDIFP | GTYQTLEMFP | RTPGIWLLHC | HVTDHIHAGM |
| 1060 | 1065 | |||
| ETTYTVLQNE | DTKSG |
Data source: UniProt
Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs
Uniprot Database Entry PhosphoSitePlus ®
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Phosphorylation Acetylation Ubiquitylation Other
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Assay Details for CPTAC-660 Collapse assay details
Data source: Panorama
Official Gene Symbol
CP
Peptide Modified Sequence
EHEGAIYPDN[+1.0]TTDFQR
Modification Type
Deamidated (NQ)
Protein - Site of Modification
138
Peptide - Site of Modification
10
Peptide Start
129
Peptide End
144
CPTAC ID
CPTAC-660
Peptide Molecular Mass
1,892.8176
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N-linked glycopeptide solid phase extraction
Matrix
serum
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Q-Exactive (ThermoFisher)
Internal Standard
synthetic peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)
Column Packing
Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)
Column Dimensions
300um x 5mm (Trap); 75um x 25cm (Analytical)
Flow Rate
0.5 uL/min
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV
| n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y8 (1+) | 15.2 | 12.1 | 12.9 | 15 | 10.2 | 15.2 | 21.4 | 15.8 | 19.9 | 15 | 15 | 15 |
| y7 (1+) | 12.6 | 7.8 | 10.5 | 13.6 | 7.6 | 13.5 | 18.5 | 10.9 | 17.1 | 15 | 15 | 15 |
| b6 (1+) | 13.6 | 11.1 | 12.3 | 15.3 | 10.5 | 14.8 | 20.5 | 15.3 | 19.2 | 15 | 15 | 15 |
| sum | 13.4 | 9.9 | 11.6 | 14.2 | 9.1 | 14.2 | 19.5 | 13.4 | 18.3 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-3505 Collapse assay details
Data source: Panorama
Official Gene Symbol
Cp
Peptide Sequence
DIFTGLIGPMK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
543
Peptide End
553
CPTAC ID
non-CPTAC-3505
Peptide Molecular Mass
1,190.6369
Species
Mus musculus (Mouse)
Assay Type
Direct PRM
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 K
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
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y4 (1+) | 3.9 | 2.2 | 2.3 | 13.3 | 3.8 | 9.6 | 13.9 | 4.4 | 9.9 | 15 | 15 | 15 |
| y8 (1+) | 3.1 | 2.6 | 2.1 | 12.1 | 5.3 | 6 | 12.5 | 5.9 | 6.4 | 15 | 15 | 15 |
| y9 (1+) | 1 | 0.9 | 2.2 | 11.9 | 2.6 | 6.7 | 11.9 | 2.8 | 7.1 | 15 | 15 | 15 |
| b2 (1+) | 2.7 | 2.5 | 1.9 | 11.7 | 4.5 | 6.1 | 12 | 5.1 | 6.4 | 15 | 15 | 15 |
| y9 (2+) | 3 | 2.7 | 3.5 | 19 | 3.6 | 7.5 | 19.2 | 4.5 | 8.3 | 15 | 15 | 15 |
| sum | 1.6 | 0.8 | 1.4 | 12.6 | 2.9 | 6.4 | 12.7 | 3 | 6.6 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-1094 Collapse assay details
Data source: Panorama
Official Gene Symbol
CP
Peptide Sequence
GAYPLSIEPIGVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
469
Peptide End
481
CPTAC ID
non-CPTAC-1094
Peptide Molecular Mass
1,370.7558
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6490 Triple Quad (Agilent)
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
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y10 (2+) | 7.3 | 3.6 | 4.7 | 11.2 | 6.2 | 4.6 | 13.4 | 7.2 | 6.6 | 15 | 15 | 15 |
| y11 (2+) | 9.5 | 5.2 | 5 | 12 | 7.3 | 6.4 | 15.3 | 9 | 8.1 | 15 | 15 | 15 |
| y5 (1+) | 5.6 | 2.8 | 4.5 | 12.9 | 5.5 | 4.5 | 14.1 | 6.2 | 6.4 | 15 | 15 | 15 |
| y8 (1+) | 5.5 | 4.6 | 7.1 | 9.1 | 5.9 | 8.5 | 10.6 | 7.5 | 11.1 | 15 | 15 | 15 |
| y10 (1+) | 9.2 | 2.1 | 4.6 | 10.9 | 4.3 | 3.3 | 14.3 | 4.8 | 5.7 | 15 | 15 | 15 |
| sum | 4.5 | 2.1 | 3.5 | 9.7 | 5.2 | 3.7 | 10.7 | 5.6 | 5.1 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-1093 Collapse assay details
Data source: Panorama
Official Gene Symbol
CP
Peptide Sequence
IYHSHIDAPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
178
Peptide End
187
CPTAC ID
non-CPTAC-1093
Peptide Molecular Mass
1,179.6037
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
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
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| b6 (2+) | 17 | 9 | 7.9 | 16.7 | 13.1 | 9.5 | 23.8 | 15.9 | 12.4 | 15 | 15 | 15 |
| y7 (2+) | 6.2 | 3.5 | 4.8 | 10.7 | 13.8 | 6.1 | 12.4 | 14.2 | 7.8 | 15 | 15 | 15 |
| y8 (2+) | 5.3 | 3.6 | 3.4 | 8 | 6.4 | 3.8 | 9.6 | 7.3 | 5.1 | 15 | 15 | 15 |
| y9 (2+) | 5.8 | 3.7 | 3.8 | 14.1 | 9.9 | 4.6 | 15.2 | 10.6 | 6 | 15 | 15 | 15 |
| y2 (1+) | 4.5 | 4 | 4 | 10.4 | 6.6 | 5.9 | 11.3 | 7.7 | 7.1 | 15 | 15 | 15 |
| sum | 3.2 | 2.2 | 2.5 | 9.3 | 7 | 3.3 | 9.8 | 7.3 | 4.1 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5587 Collapse assay details
Data source: Panorama
Official Gene Symbol
Cp
Peptide Sequence
IYHSHVDAPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
177
Peptide End
186
CPTAC ID
non-CPTAC-5587
Peptide Molecular Mass
1,165.5880
Species
Mus musculus (Mouse)
Assay Type
Direct PRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>80%
Peptide Standard Label Type
13C and 15N at C-terminus K
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
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y6 (3+) | 18.7 | 17.2 | 22.3 | 25.4 | 18.9 | 27 | 31.5 | 25.6 | 35 | 15 | 15 | 15 |
| y8 (2+) | 22.4 | 10.5 | 8.7 | 22.1 | 11.2 | 8.5 | 31.5 | 15.4 | 12.2 | 15 | 15 | 15 |
| y9 (2+) | 12.9 | 6.5 | 8 | 18.3 | 7.3 | 11.2 | 22.4 | 9.8 | 13.8 | 15 | 15 | 15 |
| y3 (1+) | 11.3 | 8.6 | 9.6 | 14.2 | 7.8 | 9.9 | 18.1 | 11.6 | 13.8 | 15 | 15 | 15 |
| y7 (1+) | 22.1 | 14.3 | 13.9 | 25.4 | 12.5 | 14.4 | 33.7 | 19 | 20 | 15 | 15 | 15 |
| sum | 8.9 | 4.6 | 5.5 | 15.2 | 5.6 | 7.4 | 17.6 | 7.2 | 9.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-1095 Collapse assay details
Data source: Panorama
Official Gene Symbol
CP
Peptide Sequence
NNEGTYYSPNYNPQSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
485
Peptide End
500
CPTAC ID
non-CPTAC-1095
Peptide Molecular Mass
1,902.8133
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6490 Triple Quad (Agilent)
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
Assay Multiplexing Expand assay panel
Johns Hopkins University-A
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| b3 (1+) | 46.2 | 10.7 | 8.1 | 88.4 | 17 | 11.2 | 99.7 | 20.1 | 13.8 | 8 | 15 | 14 |
| y8 (2+) | 9.6 | 3.5 | 4.7 | 12.9 | 2.6 | 7.1 | 16.1 | 4.4 | 8.5 | 15 | 15 | 15 |
| y9 (2+) | 19.7 | 7.6 | 6.2 | 18.5 | 8.8 | 8 | 27 | 11.6 | 10.1 | 15 | 15 | 15 |
| y4 (1+) | 19.8 | 5.7 | 5.4 | 19.8 | 9.4 | 5.4 | 28 | 11 | 7.6 | 15 | 15 | 15 |
| y6 (1+) | 15.6 | 8.6 | 6.4 | 23 | 12.2 | 6.4 | 27.8 | 14.9 | 9.1 | 13 | 15 | 15 |
| sum | 8.4 | 2.6 | 3.4 | 17.9 | 4.4 | 5.4 | 19.8 | 5.1 | 6.4 | 15 | 15 | 15 |