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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.

PECAM1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PECAM1 N/A
Sequence Length (AA) Molecular Weight (Da)
738 82522
Protein Name
Platelet endothelial cell adhesion molecule
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MQPRWAQGAT MWLGVLLTLL LCSSLEGQEN SFTINSVDMK SLPDWTVQNG
60 70 80 90 100
KNLTLQCFAD VSTTSHVKPQ HQMLFYKDDV LFYNISSMKS TESYFIPEVR
110 120 130 140 150
IYDSGTYKCT VIVNNKEKTT AEYQVLVEGV PSPRVTLDKK EAIQGGIVRV
160 170 180 190 200
NCSVPEEKAP IHFTIEKLEL NEKMVKLKRE KNSRDQNFVI LEFPVEEQDR
210 220 230 240 250
VLSFRCQARI ISGIHMQTSE STKSELVTVT ESFSTPKFHI SPTGMIMEGA
260 270 280 290 300
QLHIKCTIQV THLAQEFPEI IIQKDKAIVA HNRHGNKAVY SVMAMVEHSG
310 320 330 340 350
NYTCKVESSR ISKVSSIVVN ITELFSKPEL ESSFTHLDQG ERLNLSCSIP
360 370 380 390 400
GAPPANFTIQ KEDTIVSQTQ DFTKIASKSD SGTYICTAGI DKVVKKSNTV
410 420 430 440 450
QIVVCEMLSQ PRISYDAQFE VIKGQTIEVR CESISGTLPI SYQLLKTSKV
460 470 480 490 500
LENSTKNSND PAVFKDNPTE DVEYQCVADN CHSHAKMLSE VLRVKVIAPV
510 520 530 540 550
DEVQISILSS KVVESGEDIV LQCAVNEGSG PITYKFYREK EGKPFYQMTS
560 570 580 590 600
NATQAFWTKQ KASKEQEGEY YCTAFNRANH ASSVPRSKIL TVRVILAPWK
610 620 630 640 650
KGLIAVVIIG VIIALLIIAA KCYFLRKAKA KQMPVEMSRP AVPLLNSNNE
660 670 680 690 700
KMSDPNMEAN SHYGHNDDVR NHAMKPINDN KEPLNSDVQY TEVQVSSAES
710 720 730 738
HKDLGKKDTE TVYSEVRKAV PDAVESRYSR TEGSLDGT

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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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-5858 Collapse assay details

Data source: Panorama

Official Gene Symbol
PECAM1
Peptide Sequence
DQNFVILEFPVEEQDR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
185
Peptide End
200
CPTAC ID
CPTAC-5858
Peptide Molecular Mass
1,976.9480
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
Frozen breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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
y7 (1+) 26.2 37.3 21.5 61.6 115.4 123.2 66.9 121.3 125.1 15 17 15
b8 (1+) 18.6 45.5 43.7 61.4 118.4 136.6 64.2 126.8 143.4 15 17 15
y7 (2+) 30.2 25 30.7 70.4 106.8 113.3 76.6 109.7 117.4 15 17 15
y5 (1+) 30.8 39.7 21.8 56 127.9 100.2 63.9 133.9 102.5 15 17 15
sum 23.9 28.7 22.2 62.5 111.8 117.3 66.9 115.4 119.4 15 17 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-5949 Collapse assay details

Data source: Panorama

Official Gene Symbol
PECAM1
Peptide Sequence
DQNFVILEFPVEEQDR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
185
Peptide End
200
CPTAC ID
CPTAC-5949
Peptide Molecular Mass
1,976.9480
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 at C-terminus R
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

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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

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
b8 (1+) 14 9.2 8 9.8 13 13.5 17.1 15.9 15.7 13 25 14
y7 (1+) 7.7 4.7 7 8.8 10.3 10.4 11.7 11.3 12.5 13 25 14
y5 (1+) 8.3 6.2 6.2 8.8 11.3 15.8 12.1 12.9 17 13 25 14
y8 (2+) 7.6 7.8 9.1 9.9 11.4 9.6 12.5 13.8 13.2 13 25 14
y7 (2+) 6.9 4.9 6.2 6.6 10.8 9 9.5 11.9 10.9 13 25 14
sum 6.7 4 6.1 7.4 10.2 10 10 11 11.7 13 25 14

Additional Resources and Comments

Resources
Download SOPs
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View Protein in Panorama
Comments

Assay Details for CPTAC-2602 Collapse assay details

Data source: Panorama

Official Gene Symbol
PECAM1
Peptide Modified Sequence
DDVLFYN[+1.0]ISSM[+16.0]K
Modification Type
Deamidated (N), Oxidation (M)
Protein - Site of Modification
84, 88
Peptide - Site of Modification
7, 11
Peptide Start
78
Peptide End
89
CPTAC ID
CPTAC-2602
Peptide Molecular Mass
1,447.6541
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
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
y5 (1+) 24.2 18 13.6 30 16.3 16.9 38.5 24.3 21.7 15 15 15
y4 (1+) 15.2 9.4 9.9 16.9 16.1 10 22.7 18.6 14.1 15 15 15
b4 (1+) 38.4 14.3 10.4 32.1 17.7 9.9 50 22.8 14.4 15 15 15
sum 13.7 7.9 7 15.4 14.8 7.3 20.6 16.8 10.1 15 15 15

Additional Resources and Comments

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