DDX1, CPTAC-190 - 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
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAAFSEMGVM | PEIAQAVEEM | DWLLPTDIQA | ESIPLILGGG | DVLMAAETGS |
| 60 | 70 | 80 | 90 | 100 |
| GKTGAFSIPV | IQIVYETLKD | QQEGKKGKTT | IKTGASVLNK | WQMNPYDRGS |
| 110 | 120 | 130 | 140 | 150 |
| AFAIGSDGLC | CQSREVKEWH | GCRATKGLMK | GKHYYEVSCH | DQGLCRVGWS |
| 160 | 170 | 180 | 190 | 200 |
| TMQASLDLGT | DKFGFGFGGT | GKKSHNKQFD | NYGEEFTMHD | TIGCYLDIDK |
| 210 | 220 | 230 | 240 | 250 |
| GHVKFSKNGK | DLGLAFEIPP | HMKNQALFPA | CVLKNAELKF | NFGEEEFKFP |
| 260 | 270 | 280 | 290 | 300 |
| PKDGFVALSK | APDGYIVKSQ | HSGNAQVTQT | KFLPNAPKAL | IVEPSRELAE |
| 310 | 320 | 330 | 340 | 350 |
| QTLNNIKQFK | KYIDNPKLRE | LLIIGGVAAR | DQLSVLENGV | DIVVGTPGRL |
| 360 | 370 | 380 | 390 | 400 |
| DDLVSTGKLN | LSQVRFLVLD | EADGLLSQGY | SDFINRMHNQ | IPQVTSDGKR |
| 410 | 420 | 430 | 440 | 450 |
| LQVIVCSATL | HSFDVKKLSE | KIMHFPTWVD | LKGEDSVPDT | VHHVVVPVNP |
| 460 | 470 | 480 | 490 | 500 |
| KTDRLWERLG | KSHIRTDDVH | AKDNTRPGAN | SPEMWSEAIK | ILKGEYAVRA |
| 510 | 520 | 530 | 540 | 550 |
| IKEHKMDQAI | IFCRTKIDCD | NLEQYFIQQG | GGPDKKGHQF | SCVCLHGDRK |
| 560 | 570 | 580 | 590 | 600 |
| PHERKQNLER | FKKGDVRFLI | CTDVAARGID | IHGVPYVINV | TLPDEKQNYV |
| 610 | 620 | 630 | 640 | 650 |
| HRIGRVGRAE | RMGLAISLVA | TEKEKVWYHV | CSSRGKGCYN | TRLKEDGGCT |
| 660 | 670 | 680 | 690 | 700 |
| IWYNEMQLLS | EIEEHLNCTI | SQVEPDIKVP | VDEFDGKVTY | GQKRAAGGGS |
| 710 | 720 | 730 | 740 | |
| YKGHVDILAP | TVQELAALEK | EAQTSFLHLG | YLPNQLFRTF |
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-191 Collapse assay details
Data source: Panorama
Official Gene Symbol
DDX1
Peptide Sequence
GHVDILAPTVQELAALEK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
703
Peptide End
720
CPTAC ID
CPTAC-191
Peptide Molecular Mass
1,903.0415
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
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
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 |
| y6 (1+) | 9.4 | 5.6 | 9.8 | 20.2 | 7.3 | 12.3 | 22.3 | 9.2 | 15.7 | 25 | 15 | 15 |
| y7 (1+) | 13.9 | 6.2 | 11.5 | 15.9 | 9.1 | 18.1 | 21.1 | 11 | 21.4 | 25 | 15 | 15 |
| y8 (1+) | 15.9 | 14.2 | 6.2 | 18.5 | 14.5 | 22.6 | 24.4 | 20.3 | 23.4 | 25 | 15 | 15 |
| sum | 10 | 3.5 | 5.4 | 13.7 | 4.6 | 13.5 | 17 | 5.8 | 14.5 | 25 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-190 Collapse assay details
Data source: Panorama
Official Gene Symbol
DDX1
Peptide Modified Sequence
GSAFAIGSDGLC[+57.0]C[+57.0]QSR
Modification Type
Carbamidomethyl Cysteine, Carbamidomethyl Cysteine
Protein - Site of Modification
110, 111
Peptide - Site of Modification
12, 13
Peptide Start
99
Peptide End
114
CPTAC ID
CPTAC-190
Peptide Molecular Mass
1,684.7297
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
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
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+) | 9.5 | 10.3 | 11 | 13.2 | 11.7 | 7 | 16.3 | 15.6 | 13 | 15 | 25 | 15 |
| y9 (1+) | 30.3 | 11.2 | 12.4 | 20.1 | 10.8 | 12 | 36.4 | 15.6 | 17.3 | 15 | 25 | 15 |
| y7 (1+) | 26.3 | 15.8 | 11.7 | 29.6 | 14.9 | 9.7 | 39.6 | 21.7 | 15.2 | 15 | 25 | 15 |
| sum | 9.7 | 9.5 | 10.8 | 11.4 | 10.7 | 6.6 | 15 | 14.3 | 12.7 | 15 | 25 | 15 |