EPCAM, CPTAC-502 - CPTAC Assay Portal (original) (raw)
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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.
Overview Data source: UniProt
| Official Gene Symbol | Other Aliases |
|---|---|
| EPCAM | GA733-2, M1S2, M4S1, MIC18, TACSTD1, TROP1 |
| Sequence Length (AA) | Molecular Weight (Da) |
|---|---|
| 314 | 34932 |
| Protein Name |
|---|
| Epithelial cell adhesion molecule |
| Sources | |
|---|---|
| UniProt PhosphoSitePlus ® GeneCards | Human Protein Atlas |
Protein Sequence hover to view complete sequence
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAPPQVLAFG | LLLAAATATF | AAAQEECVCE | NYKLAVNCFV | NNNRQCQCTS |
| 60 | 70 | 80 | 90 | 100 |
| VGAQNTVICS | KLAAKCLVMK | AEMNGSKLGR | RAKPEGALQN | NDGLYDPDCD |
| 110 | 120 | 130 | 140 | 150 |
| ESGLFKAKQC | NGTSMCWCVN | TAGVRRTDKD | TEITCSERVR | TYWIIIELKH |
| 160 | 170 | 180 | 190 | 200 |
| KAREKPYDSK | SLRTALQKEI | TTRYQLDPKF | ITSILYENNV | ITIDLVQNSS |
| 210 | 220 | 230 | 240 | 250 |
| QKTQNDVDIA | DVAYYFEKDV | KGESLFHSKK | MDLTVNGEQL | DLDPGQTLIY |
| 260 | 270 | 280 | 290 | 300 |
| YVDEKAPEFS | MQGLKAGVIA | VIVVVVIAVV | AGIVVLVISR | KKRMAKYEKA |
| 310 | 314 | |||
| EIKEMGEMHR | ELNA |
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-503 Collapse assay details
Data source: Panorama
Official Gene Symbol
EPCAM
Peptide Modified Sequence
AKPEGALQNNDGLYDPDC[+57.0]DESGLFK
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
99
Peptide - Site of Modification
18
Peptide Start
82
Peptide End
106
CPTAC ID
CPTAC-503
Peptide Molecular Mass
2,752.2286
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
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 (1+) | 21.1 | 7.7 | 13.7 | 28.5 | 14.3 | 20.3 | 35.5 | 16.2 | 24.5 | 15 | 25 | 15 |
| y9 (1+) | 50.6 | 22.6 | 33.1 | 58.2 | 21.3 | 44.8 | 77.1 | 31.1 | 55.7 | 15 | 25 | 15 |
| y8 (1+) | 35.6 | 23 | 14.1 | 37 | 26.2 | 28.6 | 51.3 | 34.9 | 31.9 | 15 | 25 | 15 |
| sum | 22.6 | 8.4 | 11.5 | 28.6 | 14 | 20.2 | 36.5 | 16.3 | 23.2 | 15 | 25 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-502 Collapse assay details
Data source: Panorama
Official Gene Symbol
EPCAM
Peptide Modified Sequence
LAVNC[+57.0]FVNNNR
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
38
Peptide - Site of Modification
5
Peptide Start
34
Peptide End
44
CPTAC ID
CPTAC-502
Peptide Molecular Mass
1,319.6405
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
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+) | 29 | 9.7 | 11.6 | 44.7 | 9.6 | 14.6 | 53.3 | 13.6 | 18.6 | 15 | 25 | 15 |
| y7 (1+) | 29.5 | 10.4 | 11.6 | 43.7 | 10.3 | 18.4 | 52.7 | 14.6 | 21.8 | 15 | 25 | 15 |
| y6 (1+) | 28.1 | 11.9 | 8 | 69.1 | 22.1 | 10.1 | 74.6 | 25.1 | 12.9 | 15 | 25 | 15 |
| sum | 27.6 | 10.3 | 8.7 | 68 | 15 | 12.6 | 73.4 | 18.2 | 15.3 | 15 | 25 | 15 |