Dek, CPTAC-3786 - 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.
Protein Sequence hover to view complete sequence
non-CPTAC-3786: View additional IHFFLSK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MSAAAAPAAE | GEDAPVPPSS | EKEPEMPGPR | EESEEEEEDD | EDDDEEDEEE |
| 60 | 70 | 80 | 90 | 100 |
| EKEKSLIVEG | KREKKKVERL | TMQVSSLQRE | PFTVTQGKGQ | KLCEIERIHF |
| 110 | 120 | 130 | 140 | 150 |
| FLSKKKPDEL | RNLHKLLYNR | PGTVSSLKKN | VGQFSGFPFE | KGSTQYKKKE |
| 160 | 170 | 180 | 190 | 200 |
| EMLKKFRNAM | LKSICEVLDL | ERSGVNSELV | KRILNFLMHP | KPSGKPLPKS |
| 210 | 220 | 230 | 240 | 250 |
| KKSSSKGSKK | ERNSSGTTRK | SKQTKCPEIL | SDESSSDEDE | KKNKEESSED |
| 260 | 270 | 280 | 290 | 300 |
| EEKESEEEQP | PKKTSKKEKA | KQKATAKSKK | SVKSANVKKA | DSSTTKKNQK |
| 310 | 320 | 330 | 340 | 350 |
| SSKKESESED | SSDDEPLIKK | LKKPPTDEEL | KETVKKLLAD | ANLEEVTMKQ |
| 360 | 370 | 380 | ||
| ICKEVYENYP | AYDLTERKDF | IKTTVKELIS |
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 non-CPTAC-3786 Collapse assay details
Data source: Panorama
Official Gene Symbol
Dek
Peptide Sequence
IHFFLSK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
98
Peptide End
104
CPTAC ID
non-CPTAC-3786
Peptide Molecular Mass
890.5014
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
>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
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+) | 9.7 | 6.8 | 4.5 | 9.5 | 8.6 | 7.3 | 13.6 | 11 | 8.6 | 15 | 15 | 15 |
| y5 (3+) | 84.5 | 97.3 | 91.1 | 128.5 | 88.6 | 105.5 | 153.8 | 131.6 | 139.4 | 15 | 15 | 15 |
| y6 (2+) | 26.3 | 8.1 | 4.5 | 23.8 | 9.2 | 10.2 | 35.5 | 12.3 | 11.1 | 15 | 15 | 15 |
| y2 (1+) | 7.3 | 3.1 | 2.2 | 10.2 | 4.4 | 4.7 | 12.5 | 5.4 | 5.2 | 15 | 15 | 15 |
| y3 (1+) | 12 | 4.7 | 3.3 | 15.5 | 7.8 | 6.3 | 19.6 | 9.1 | 7.1 | 15 | 15 | 15 |
| sum | 6.9 | 3.3 | 2.6 | 8 | 5.6 | 5.5 | 10.6 | 6.5 | 6.1 | 15 | 15 | 15 |