Ncam1, CPTAC-3846 - 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

non-CPTAC-3846: View additional GLGEISAATEFK data

10 20 30 40 50
MLRTKDLIWT LFFLGTAVSL QVDIVPSQGE ISVGESKFFL CQVAGDAKDK
60 70 80 90 100
DISWFSPNGE KLSPNQQRIS VVWNDDDSST LTIYNANIDD AGIYKCVVTA
110 120 130 140 150
EDGTQSEATV NVKIFQKLMF KNAPTPQEFK EGEDAVIVCD VVSSLPPTII
160 170 180 190 200
WKHKGRDVIL KKDVRFIVLS NNYLQIRGIK KTDEGTYRCE GRILARGEIN
210 220 230 240 250
FKDIQVIVNV PPTVQARQSI VNATANLGQS VTLVCDADGF PEPTMSWTKD
260 270 280 290 300
GEPIENEEED DEKHIFSDDS SELTIRNVDK NDEAEYVCIA ENKAGEQDAS
310 320 330 340 350
IHLKVFAKPK ITYVENQTAM ELEEQVTLTC EASGDPIPSI TWRTSTRNIS
360 370 380 390 400
SEEKTLDGHM VVRSHARVSS LTLKSIQYTD AGEYICTASN TIGQDSQSMY
410 420 430 440 450
LEFQYAPKLQ GPVAVYTWEG NQVNITCEVF AYPSATISWF RDGQLLPSSN
460 470 480 490 500
YSNIKIYNTP SASYLEVTPD SENDFGNYNC TAVNRIGQES LEFILVQADT
510 520 530 540 550
PSSPSIDRVE PYSSTAQVQF DEPEATGGVP ILKYKAEWKS LGEESWHFKW
560 570 580 590 600
YDAKEANMEG IVTIMGLKPE TRYSVRLAAL NGKGLGEISA ATEFKTQPVR
610 620 630 640 650
EPSAPKLEGQ MGEDGNSIKV NLIKQDDGGS PIRHYLVKYR ALASEWKPEI
660 670 680 690 700
RLPSGSDHVM LKSLDWNAEY EVYVVAENQQ GKSKAAHFVF RTSAQPTAIP
710 720 730 740 750
ANGSPTAGLS TGAIVGILIV IFVLLLVVMD ITCYFLNKCG LLMCIAVNLC
760 770 780 790 800
GKAGPGAKGK DMEEGKAAFS KDESKEPIVE VRTEEERTPN HDGGKHTEPN
810 820 830 840 850
ETTPLTEPEL PADTTATVED MLPSVTTVTT NSDTITETFA TAQNSPTSET
860 870 880 890 900
TTLTSSIAPP ATTVPDSNSV PAGQATPSKG VTASSSSPAS APKVAPLVDL
910 920 930 940 950
SDTPTSAPSA SNLSSTVLAN QGAVLSPSTP ASAGETSKAP PASKASPAPT
960 970 980 990 1000
PTPAGAASPL AAVAAPATDA PQAKQEAPST KGPDPEPTQP GTVKNPPEAA
1010 1020 1030 1040 1050
TAPASPKSKA ATTNPSQGED LKMDEGNFKT PDIDLAKDVF AALGSPRPAT
1060 1070 1080 1090 1100
GASGQASELA PSPADSAVPP APAKTEKGPV ETKSEPPESE AKPAPTEVKT
1110 1115
VPNDATQTKE NESKA

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-6212 Collapse assay details

Data source: Panorama

Official Gene Symbol

NCAM1

Peptide Sequence

GLGEISAASEFK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

7

Peptide Start

593

Peptide End

604

CPTAC ID

CPTAC-6212

Peptide Molecular Mass

1,207.6085

Species

Homo Sapiens

Assay Type

Enrichment MRM

Enrichment Method

IMAC

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 K

LC

Eksigent

Column Packing

Reprosil C18, 3um

Column Dimensions

75µm x 15cm

Flow Rate

0.3 µL/min

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 | | y6 (1+) | 7.2 | 3.7 | 2.7 | 6.9 | 4.8 | 6.8 | 10 | 6.1 | 7.3 | 15 | 15 | 15 | | y8 (1+) | 6.3 | 5.8 | 2.6 | 8.7 | 4.6 | 6.9 | 10.7 | 7.4 | 7.4 | 15 | 15 | 15 | | y10 (1+) | 8.2 | 4.5 | 3.5 | 9.2 | 5 | 6.5 | 12.3 | 6.7 | 7.4 | 15 | 15 | 15 | | y7 (1+) | 9.1 | 3.1 | 3 | 8.5 | 3.5 | 6 | 12.5 | 4.7 | 6.7 | 15 | 15 | 15 | | sum | 7.6 | 3.5 | 2.8 | 8.2 | 3.2 | 6.3 | 11.2 | 4.7 | 6.9 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3846 Collapse assay details

Data source: Panorama

Official Gene Symbol

Ncam1

Peptide Sequence

GLGEISAATEFK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

584

Peptide End

595

CPTAC ID

non-CPTAC-3846

Peptide Molecular Mass

1,221.6241

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

>80%

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

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 | | y10 (1+) | 15 | 5.7 | 5.3 | 13.5 | 7.1 | 7.4 | 20.2 | 9.1 | 9.1 | 15 | 15 | 15 | | y8 (1+) | 9.2 | 5.6 | 3.8 | 10.5 | 6 | 7.1 | 14 | 8.2 | 8.1 | 15 | 15 | 15 | | y7 (1+) | 11.9 | 5.4 | 4.5 | 13.6 | 9.7 | 5.1 | 18.1 | 11.1 | 6.8 | 15 | 15 | 15 | | y4 (1+) | 35.6 | 7.8 | 5.5 | 35.6 | 8.8 | 6.4 | 50.3 | 11.8 | 8.4 | 15 | 15 | 15 | | y5 (2+) | 51.1 | 45.4 | 78.1 | 82.8 | 46.9 | 95.1 | 97.3 | 65.3 | 123.1 | 15 | 15 | 15 | | sum | 6.3 | 2.1 | 1.3 | 8.4 | 5.8 | 3.4 | 10.5 | 6.2 | 3.6 | 15 | 15 | 15 |

Additional Resources and Comments