Vcam1, CPTAC-3397 - 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

CPTAC-5950: View additional TQIDSPLSGK data

non-CPTAC-3397: View additional LHIDQIDSTLK data

Data source: UniProt

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node

to view detailed assay information below

All other points link out to UniProt

Phosphorylation Acetylation Ubiquitylation Other

loading

Assay Details for CPTAC-5950 Collapse assay details

Data source: Panorama

Official Gene Symbol

VCAM1

Peptide Sequence

TQIDSPLSGK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

4

Peptide Start

349

Peptide End

358

CPTAC ID

CPTAC-5950

Peptide Molecular Mass

1,044.5451

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

N/A

Matrix

FFPE tumor tissue lysate pool

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

QTRAP 5500

Internal Standard

peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N K

LC

Eksigent nanoLC 425

Column Packing

3 µm ChromXP C18EP, 120 Å

Column Dimensions

150 x 0.3 mm

Flow Rate

0.3 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 | | y8 (1+) | 8.1 | 4.2 | 2.5 | 11.2 | 12.5 | 13.8 | 13.8 | 13.2 | 14 | 13 | 25 | 14 | | y7 (1+) | 10 | 4.3 | 2.9 | 11.8 | 12.9 | 14.1 | 15.5 | 13.6 | 14.4 | 13 | 25 | 14 | | y6 (1+) | 10.9 | 5.9 | 6.4 | 13.9 | 11.3 | 14.3 | 17.7 | 12.7 | 15.7 | 13 | 25 | 14 | | b3 (1+) | 8.4 | 7.6 | 4.1 | 7.5 | 9.8 | 11.9 | 11.3 | 12.4 | 12.6 | 13 | 25 | 14 | | y3 (1+) | 10.8 | 9.4 | 8 | 16.3 | 15 | 19.3 | 19.6 | 17.7 | 20.9 | 13 | 25 | 14 | | y5 (1+) | 16.2 | 8.8 | 9.2 | 18.7 | 16.3 | 14 | 24.7 | 18.5 | 16.8 | 13 | 25 | 14 | | sum | 7.3 | 3.8 | 2.4 | 10.1 | 12 | 13.6 | 12.5 | 12.6 | 13.8 | 13 | 25 | 14 |

Additional Resources and Comments

Assay Details for non-CPTAC-3397 Collapse assay details

Data source: Panorama

Official Gene Symbol

Vcam1

Peptide Sequence

LHIDQIDSTLK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

199

Peptide End

209

CPTAC ID

non-CPTAC-3397

Peptide Molecular Mass

1,281.6929

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

>95%

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 | | b5 (1+) | 7.5 | 5.8 | 6 | 15.4 | 6.1 | 7.9 | 17.1 | 8.4 | 9.9 | 15 | 15 | 15 | | b2 (1+) | 6.9 | 6 | 7.4 | 12.6 | 3.6 | 5.7 | 14.4 | 7 | 9.3 | 15 | 15 | 15 | | y2 (1+) | 12.6 | 6.3 | 6.7 | 16.5 | 9 | 8.1 | 20.8 | 11 | 10.5 | 15 | 15 | 15 | | y4 (1+) | 7.9 | 7.6 | 6.2 | 17 | 10.4 | 10.4 | 18.7 | 12.9 | 12.1 | 15 | 15 | 15 | | y5 (1+) | 6.2 | 6.3 | 9.1 | 14.2 | 8.1 | 8.9 | 15.5 | 10.3 | 12.7 | 15 | 15 | 15 | | sum | 3.1 | 4.6 | 3.8 | 13.3 | 5.3 | 4.5 | 13.7 | 7 | 5.9 | 15 | 15 | 15 |

Additional Resources and Comments