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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.

Vcam1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
Vcam1 Vcam-1
Sequence Length (AA) Molecular Weight (Da)
739 81317
Protein Name
Vascular cell adhesion protein 1
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MPVKMVAVLG ASTVLWILFA VSQAFKIEIS PEYKTIAQIG DSMALTCSTT
60 70 80 90 100
GCESPLFSWR TQIDSPLNAK VRTEGSKSVL TMEPVSFENE HSYLCTATCG
110 120 130 140 150
SGKLERSIHV DIYSFPKDPE IQFSGPLEVG KPVTVKCLAP DIYPVYRLEI
160 170 180 190 200
DLFKGDQLMN RQEFSSEEMT KSLETKSLEV TFTPVIEDIG KALVCRAKLH
210 220 230 240 250
IDQIDSTLKE RETVKELQVY ISPRNTTISV HPSTRLQEGG AVTMTCSSEG
260 270 280 290 300
LPAPEIFWGR KLDNEVLQLL SGNATLTLIA MRMEDSGVYV CEGVNLIGRD
310 320 330 340 350
KAEVELVVQE KPFIVDISPG SQVAAQVGDS VVLTCAAIGC DSPSFSWRTQ
360 370 380 390 400
TDSPLNGVVR NEGAKSTLVL SSVGFEDEHS YLCAVTCLQR TLEKRTQVEV
410 420 430 440 450
YSFPEDPVIK MSGPLVHGRP VTVNCTVPNV YPFDHLEIEL LKGETTLMKK
460 470 480 490 500
YFLEEMGIKS LETKILETTF IPTIEDTGKS LVCLARLHSG EMESEPKQRQ
510 520 530 540 550
SVQPLYVNVA PKETTIWVSP SPILEEGSPV NLTCSSDGIP APKILWSRQL
560 570 580 590 600
NNGELQPLSE NTTLTFMSTK RDDSGIYVCE GINEAGISRK SVELIIQVSP
610 620 630 640 650
KDIQLTVFPS KSVKEGDTVI ISCTCGNVPE TWIILKKKAK TGDMVLKSVD
660 670 680 690 700
GSYTIRQAQL QDAGIYECES KTEVGSQLRS LTLDVKGKEH NKDYFSPELL
710 720 730 739
ALYCASSLVI PAIGMIVYFA RKANMKGSYS LVEAQKSKV

Data source: UniProt

Protein Map Collapse protein map

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-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

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 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

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
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

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view larger image
view larger image

Response Curves

Data source: Panorama

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view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 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

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments