CD44, CPTAC-668 - 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

CPTAC-692: View additional TFIPVTSAK data

10 20 30 40 50
MDKFWWHAAW GLCLVPLSLA QIDLNITCRF AGVFHVEKNG RYSISRTEAA
60 70 80 90 100
DLCKAFNSTL PTMAQMEKAL SIGFETCRYG FIEGHVVIPR IHPNSICAAN
110 120 130 140 150
NTGVYILTSN TSQYDTYCFN ASAPPEEDCT SVTDLPNAFD GPITITIVNR
160 170 180 190 200
DGTRYVQKGE YRTNPEDIYP SNPTDDDVSS GSSSERSSTS GGYIFYTFST
210 220 230 240 250
VHPIPDEDSP WITDSTDRIP ATTLMSTSAT ATETATKRQE TWDWFSWLFL
260 270 280 290 300
PSESKNHLHT TTQMAGTSSN TISAGWEPNE ENEDERDRHL SFSGSGIDDD
310 320 330 340 350
EDFISSTIST TPRAFDHTKQ NQDWTQWNPS HSNPEVLLQT TTRMTDVDRN
360 370 380 390 400
GTTAYEGNWN PEAHPPLIHH EHHEEEETPH STSTIQATPS STTEETATQK
410 420 430 440 450
EQWFGNRWHE GYRQTPKEDS HSTTGTAAAS AHTSHPMQGR TTPSPEDSSW
460 470 480 490 500
TDFFNPISHP MGRGHQAGRR MDMDSSHSIT LQPTANPNTG LVEDLDRTGP
510 520 530 540 550
LSMTTQQSNS QSFSTSHEGL EEDKDHPTTS TLTSSNRNDV TGGRRDPNHS
560 570 580 590 600
EGSTTLLEGY TSHYPHTKES RTFIPVTSAK TGSFGVTAVT VGDSNSNVNR
610 620 630 640 650
SLSGDQDTFH PSGGSHTTHG SESDGHSHGS QEGGANTTSG PIRTPQIPEW
660 670 680 690 700
LIILASLLAL ALILAVCIAV NSRRRCGQKK KLVINSGNGA VEDRKPSGLN
710 720 730 740 742
GEASKSQEMV HLVNKESSET PDQFMTADET RNLQNVDMKI GV

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-692 Collapse assay details

Data source: Panorama

Official Gene Symbol

CD44

Peptide Sequence

TFIPVTSAK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

572

Peptide End

580

CPTAC ID

CPTAC-692

Peptide Molecular Mass

962.5437

Species

Homo sapiens (Human)

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

Matrix

plasma

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

Publication

View Details (opens in a new window)

Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting Western blot and ELISA. Schoenherr RM, Saul RG, Whiteaker JR, Yan P, Whiteley GR, Paulovich AG. Mol Cell Proteomics. 2015 Feb;14(2):382-98. doi: 10.1074/mcp.O114.043133. Epub 2014 Dec 15. PMID: 25512614

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

5500 Qtrap

Internal Standard

synthetic peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Eksigent NanoLC 2D

Column Packing

ReproSil-Pur C18-AQ 3 um

Column Dimensions

100 mm x 75 um ID

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

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Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y4 (1+) | 82.4 | 22.5 | 12.7 | 64.3 | 29.4 | 13.6 | 104.5 | 37 | 18.6 | 15 | 15 | 15 | | y6 (1+) | 22.3 | 4.2 | 2.2 | 29 | 4.9 | 3.6 | 36.6 | 6.5 | 4.2 | 15 | 15 | 15 | | y7 (1+) | 24.1 | 4.8 | 2.7 | 29.4 | 6 | 3.9 | 38 | 7.7 | 4.7 | 15 | 15 | 15 | | sum | 17.5 | 3.3 | 1.9 | 21.1 | 4.7 | 3.4 | 27.4 | 5.7 | 3.9 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-6214 Collapse assay details

Data source: Panorama

Official Gene Symbol

CD44

Peptide Sequence

YGFIEGHVVIPR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

7

Peptide Start

79

Peptide End

90

CPTAC ID

CPTAC-6214

Peptide Molecular Mass

1,385.7456

Species

Homo Sapiens

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

Matrix

Frozen tissue

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

QTRAP 5500

Internal Standard

Extended heavy peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Eksigent

Column Packing

Reprosil C18, 3um

Column Dimensions

75µm x 15cm

Flow Rate

0.3 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y7 (1+) | 4.6 | 3.8 | 2.7 | 9.1 | 8.1 | 3.7 | 10.2 | 8.9 | 4.6 | 15 | 15 | 15 | | y5 (1+) | 4.6 | 3.3 | 3.7 | 6.4 | 5.7 | 6.8 | 7.9 | 6.6 | 7.7 | 15 | 15 | 15 | | y4 (1+) | 4.3 | 3.3 | 2.9 | 8.5 | 5.5 | 6.5 | 9.5 | 6.4 | 7.1 | 15 | 15 | 15 | | y9 (2+) | 4.9 | 3.5 | 4.2 | 7.9 | 6.3 | 10.1 | 9.3 | 7.2 | 10.9 | 15 | 15 | 15 | | sum | 4.3 | 2.7 | 3.1 | 6.9 | 5.8 | 6.7 | 8.1 | 6.4 | 7.4 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-668 Collapse assay details

Data source: Panorama

Official Gene Symbol

CD44

Peptide Modified Sequence

AFN[+1.0]STLPTM[+16.0]AQM[+16.0]EK

Modification Type

Deamidated (NQ), Oxidation (M), Oxidation (M)

Protein - Site of Modification

57, 63, 66

Peptide - Site of Modification

3, 9, 12

Peptide Start

55

Peptide End

68

CPTAC ID

CPTAC-668

Peptide Molecular Mass

1,600.7113

Species

Homo sapiens (Human)

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

Matrix

serum

Submitting Laboratory

Johns Hopkins University

Submitting Lab PI

Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Q-Exactive (ThermoFisher)

Internal Standard

synthetic peptide

Peptide Standard Purity

Crude

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)

Column Packing

Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)

Column Dimensions

300um x 5mm (Trap); 75um x 25cm (Analytical)

Flow Rate

0.5 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y9 (1+) | 12.5 | 14.1 | 18.7 | 11.8 | 15.3 | 20.2 | 17.2 | 20.8 | 27.5 | 15 | 15 | 15 | | y8 (1+) | 4.8 | 9.3 | 5.6 | 6.2 | 8.4 | 5.5 | 7.8 | 12.5 | 7.8 | 15 | 15 | 15 | | y8 (2+) | 19.6 | 27 | 15.2 | 18 | 27.9 | 13.1 | 26.6 | 38.8 | 20.1 | 15 | 15 | 15 | | sum | 4.7 | 9.6 | 7.2 | 5.7 | 8.5 | 6.4 | 7.4 | 12.8 | 9.6 | 15 | 15 | 15 |

Additional Resources and Comments