TERF2, CPTAC-956 - 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 |
|---|---|---|---|---|
| MAAGAGTAGP | ASGPGVVRDP | AASQPRKRPG | REGGEGARRS | DTMAGGGGSS |
| 60 | 70 | 80 | 90 | 100 |
| DGSGRAAGRR | ASRSSGRARR | GRHEPGLGGP | AERGAGEARL | EEAVNRWVLK |
| 110 | 120 | 130 | 140 | 150 |
| FYFHEALRAF | RGSRYGDFRQ | IRDIMQALLV | RPLGKEHTVS | RLLRVMQCLS |
| 160 | 170 | 180 | 190 | 200 |
| RIEEGENLDC | SFDMEAELTP | LESAINVLEM | IKTEFTLTEA | VVESSRKLVK |
| 210 | 220 | 230 | 240 | 250 |
| EAAVIICIKN | KEFEKASKIL | KKHMSKDPTT | QKLRNDLLNI | IREKNLAHPV |
| 260 | 270 | 280 | 290 | 300 |
| IQNFSYETFQ | QKMLRFLESH | LDDAEPYLLT | MAKKALKSES | AASSTGKEDK |
| 310 | 320 | 330 | 340 | 350 |
| QPAPGPVEKP | PREPARQLRN | PPTTIGMMTL | KAAFKTLSGA | QDSEAAFAKL |
| 360 | 370 | 380 | 390 | 400 |
| DQKDLVLPTQ | ALPASPALKN | KRPRKDENES | SAPADGEGGS | ELQPKNKRMT |
| 410 | 420 | 430 | 440 | 450 |
| ISRLVLEEDS | QSTEPSAGLN | SSQEAASAPP | SKPTVLNQPL | PGEKNPKVPK |
| 460 | 470 | 480 | 490 | 500 |
| GKWNSSNGVE | EKETWVEEDE | LFQVQAAPDE | DSTTNITKKQ | KWTVEESEWV |
| 510 | 520 | 530 | 540 | 542 |
| KAGVQKYGEG | NWAAISKNYP | FVNRTAVMIK | DRWRTMKRLG | MN |
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-956 Collapse assay details
Data source: Panorama
Official Gene Symbol
TERF2
Peptide Modified Sequence
DLVLPTQALPAS[+80.0]PALK
Modification Type
Phospho (ST)
Protein - Site of Modification
365
Peptide - Site of Modification
12
Peptide Start
354
Peptide End
369
CPTAC ID
CPTAC-956
Peptide Molecular Mass
1,712.9114
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
QTrap 5500 (Sciex)
Internal Standard
Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm 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 |
| y12 (2+) | 46.6 | 25.3 | 22.6 | 87.2 | 32.4 | 30.8 | 98.9 | 41.1 | 38.2 | 15 | 24 | 15 |
| y13 (2+) | 46.7 | 29.7 | 18.4 | 69.8 | 33.7 | 18.4 | 84 | 44.9 | 26 | 15 | 24 | 15 |
| y7 (1+) | 44.4 | 16 | 14 | 66.5 | 25 | 15.7 | 80 | 29.7 | 21 | 15 | 24 | 15 |
| sum | 30 | 12.6 | 9.7 | 65.4 | 22.9 | 14.3 | 72 | 26.1 | 17.3 | 15 | 24 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3256 Collapse assay details
Data source: Panorama
Official Gene Symbol
TERF2
Peptide Sequence
DLVLPTQALPASPALK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
354
Peptide End
369
CPTAC ID
CPTAC-3256
Peptide Molecular Mass
1,632.9451
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/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 |
| y12 (1+) | 13.9 | 17.7 | 22.9 | 15.4 | 31.1 | 34.2 | 20.7 | 35.8 | 41.2 | 15 | 15 | 15 |
| y8 (1+) | 34.8 | 20.5 | 21.9 | 57 | 39.9 | 32.7 | 66.8 | 44.9 | 39.4 | 15 | 15 | 15 |
| y7 (1+) | 22.2 | 22.1 | 19.6 | 34.8 | 35.6 | 26.6 | 41.3 | 41.9 | 33 | 15 | 15 | 15 |
| sum | 13.9 | 15.9 | 20 | 24.1 | 31.7 | 30.8 | 27.8 | 35.5 | 36.7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3257 Collapse assay details
Data source: Panorama
Official Gene Symbol
TERF2
Peptide Modified Sequence
DLVLPTQALPAS[+80.0]PALK
Modification Type
Phospho (ST)
Protein - Site of Modification
365
Peptide - Site of Modification
12
Peptide Start
354
Peptide End
369
CPTAC ID
CPTAC-3257
Peptide Molecular Mass
1,712.9114
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/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+) | 16.9 | 29.5 | 24.3 | 25.3 | 30.6 | 33.6 | 30.4 | 42.5 | 41.5 | 15 | 15 | 15 |
| y13 (2+) | 16.5 | 26.2 | 31 | 22.4 | 30.6 | 41.7 | 27.8 | 40.3 | 52 | 15 | 15 | 15 |
| y12 (2+) | 18 | 23 | 20.8 | 18.4 | 33.3 | 32.5 | 25.7 | 40.5 | 38.6 | 15 | 15 | 15 |
| y7 (1+) | 14.4 | 26 | 27.9 | 16.7 | 32.4 | 37.3 | 22.1 | 41.5 | 46.6 | 15 | 15 | 15 |
| sum | 10.9 | 23.9 | 23.5 | 15.3 | 30.5 | 34.3 | 18.8 | 38.7 | 41.6 | 15 | 15 | 15 |