RAD9A, CPTAC-5930 - 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
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MKCLVTGGNV | KVLGKAVHSL | SRIGDELYLE | PLEDGLSLRT | VNSSRSAYAC |
| 60 | 70 | 80 | 90 | 100 |
| FLFAPLFFQQ | YQAATPGQDL | LRCKILMKSF | LSVFRSLAML | EKTVEKCCIS |
| 110 | 120 | 130 | 140 | 150 |
| LNGRSSRLVV | QLHCKFGVRK | THNLSFQDCE | SLQAVFDPAS | CPHMLRAPAR |
| 160 | 170 | 180 | 190 | 200 |
| VLGEAVLPFS | PALAEVTLGI | GRGRRVILRS | YHEEEADSTA | KAMVTEMCLG |
| 210 | 220 | 230 | 240 | 250 |
| EEDFQQLQAQ | EGVAITFCLK | EFRGLLSFAE | SANLNLSIHF | DAPGRPAIFT |
| 260 | 270 | 280 | 290 | 300 |
| IKDSLLDGHF | VLATLSDTDS | HSQDLGSPER | HQPVPQLQAH | STPHPDDFAN |
| 310 | 320 | 330 | 340 | 350 |
| DDIDSYMIAM | ETTIGNEGSR | VLPSISLSPG | PQPPKSPGPH | SEEEDEAEPS |
| 360 | 370 | 380 | 390 | 391 |
| TVPGTPPPKK | FRSLFFGSIL | APVRSPQGPS | PVLAEDSEGE | G |
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-5930 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAD9A
Peptide Sequence
SPQGPSPVLAEDSEGEG
Modification Type
unmodified
Protein - Site of Modification
375
Peptide - Site of Modification
N/A
Peptide Start
375
Peptide End
391
CPTAC ID
CPTAC-5930
Peptide Molecular Mass
1,654.7322
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Sciex 5500 QTRAP
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N L
LC
Eksigent 425
Column Packing
Reprosil
Column Dimensions
75um x 15cm
Flow Rate
300 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 |
| b15 (2+) | 47.3 | 23.2 | 35.7 | 46.5 | 26.1 | 34.6 | 66.3 | 34.9 | 49.7 | 15 | 27 | 15 |
| b8 (1+) | 36.7 | 17 | 12.6 | 26.9 | 16.6 | 14.1 | 45.5 | 23.8 | 18.9 | 15 | 27 | 15 |
| b9 (1+) | 26 | 19.8 | 20 | 30.1 | 19.9 | 26.6 | 39.8 | 28.1 | 33.3 | 15 | 27 | 15 |
| b10 (1+) | 36.4 | 18.4 | 21.2 | 54.7 | 23 | 28 | 65.7 | 29.5 | 35.1 | 15 | 27 | 15 |
| b11 (1+) | 32.7 | 29.1 | 33.6 | 40.9 | 26.2 | 28.3 | 52.4 | 39.2 | 43.9 | 15 | 27 | 15 |
| y9 (1+) | 30.3 | 23.9 | 23 | 35 | 29.6 | 43.8 | 46.3 | 38 | 49.5 | 15 | 27 | 15 |
| sum | 16.5 | 8.8 | 10.3 | 16.8 | 12.3 | 12.3 | 23.5 | 15.1 | 16 | 15 | 27 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-5931 Collapse assay details
Data source: Panorama
Official Gene Symbol
RAD9A
Peptide Modified Sequence
SPQGPSPVLAEDS[+79.966331]EGEG
Modification Type
Phospho (ST)
Protein - Site of Modification
388
Peptide - Site of Modification
13
Peptide Start
375
Peptide End
391
CPTAC ID
CPTAC-5931
Peptide Molecular Mass
1,734.6986
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
Cell Lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Sciex 5500 QTRAP
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N L
LC
Eksigent 425
Column Packing
Reprosil
Column Dimensions
75um x 15cm
Flow Rate
300 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 |
| y6-98 (1+) | 42.2 | 22.4 | 8.9 | 63.6 | 30.5 | 12.3 | 76.3 | 37.8 | 15.2 | 15 | 27 | 15 |
| b6 (1+) | 50.8 | 19.8 | 8.5 | 39.6 | 22.6 | 16.5 | 64.4 | 30 | 18.6 | 15 | 27 | 15 |
| b8 (1+) | 24.3 | 9.9 | 6.6 | 28.9 | 13 | 12 | 37.8 | 16.3 | 13.7 | 15 | 27 | 15 |
| b9 (1+) | 42.9 | 15.1 | 5.1 | 48.9 | 18.5 | 11 | 65.1 | 23.9 | 12.1 | 15 | 27 | 15 |
| b10 (1+) | 53.5 | 20.6 | 7.2 | 49.3 | 24.5 | 12.4 | 72.8 | 32 | 14.3 | 15 | 27 | 15 |
| b11 (1+) | 48.1 | 18 | 11.4 | 56.1 | 23.6 | 12.4 | 73.9 | 29.7 | 16.8 | 15 | 27 | 15 |
| b15-98 (2+) | 56.6 | 30.6 | 12.9 | 55.1 | 33.4 | 15.9 | 79 | 45.3 | 20.5 | 15 | 27 | 15 |
| sum | 19.8 | 5.6 | 2 | 23.5 | 11.9 | 10.3 | 30.7 | 13.2 | 10.5 | 15 | 27 | 15 |