Nid1, CPTAC-3848 - 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-3848: View additional YALSNSIGPVR data

10 20 30 40 50
MLDASGCSWA MWTWALLQLL LLVGPGGCLN RQELFPFGPG QGDLELEAGD
60 70 80 90 100
DVVSPSLELI GELSFYDRTD ITSVYVTTNG IIAMSEPPAT EYHPGTFPPS
110 120 130 140 150
FGSVAPFLAD LDTTDGLGNV YYREDLSPFI IQMAAEYVQR GFPEVSFQPT
160 170 180 190 200
SVVVVTWESV APYGGPSSSP AEEGKRNTFQ AVLASSNSSS YAIFLYPEDG
210 220 230 240 250
LQFFTTFSKK DESQVPAVVG FSKGLVGFLW KSNGAYNIFA NDRESIENLA
260 270 280 290 300
KSSNAGHQGV WVFEIGSPAT AKGVVSADVN LDLDDDGADY EDEDYDLVTS
310 320 330 340 350
HLGLEDVATP SPSHSPRRGY PDPHNVPRIL SPGYEATERP RGVPTERTRS
360 370 380 390 400
FQLPAERFPQ HHPQVIDVDE VEETGVVFSY NTGSQQTCAN NRHQCSVHAE
410 420 430 440 450
CRDYATGFCC RCVANYTGNG RQCVAEGSPQ RVNGKVKGRI FVGSSQVPVV
460 470 480 490 500
FENTDLHSYV VMNHGRSYTA ISTIPETVGY SLLPLAPIGG IIGWMFAVEQ
510 520 530 540 550
DGFKNGFSIT GGEFTRQAEV TFLGHPGKLV LKQQFSGIDE HGHLTISTEL
560 570 580 590 600
EGRVPQIPYG ASVHIEPYTE LYHYSSSVIT SSSTREYTVM EPDQDGAAPS
610 620 630 640 650
HTHIYQWRQT ITFQECAHDD ARPALPSTQQ LSVDSVFVLY NKEERILRYA
660 670 680 690 700
LSNSIGPVRD GSPDALQNPC YIGTHGCDSN AACRPGPGTQ FTCECSIGFR
710 720 730 740 750
GDGQTCYDID ECSEQPSRCG NHAVCNNLPG TFRCECVEGY HFSDRGTCVA
760 770 780 790 800
AEDQRPINYC ETGLHNCDIP QRAQCIYMGG SSYTCSCLPG FSGDGRACRD
810 820 830 840 850
VDECQHSRCH PDAFCYNTPG SFTCQCKPGY QGDGFRCMPG EVSKTRCQLE
860 870 880 890 900
REHILGAAGG ADAQRPTLQG MFVPQCDEYG HYVPTQCHHS TGYCWCVDRD
910 920 930 940 950
GRELEGSRTP PGMRPPCLST VAPPIHQGPV VPTAVIPLPP GTHLLFAQTG
960 970 980 990 1000
KIERLPLERN TMKKTEAKAF LHIPAKVIIG LAFDCVDKVV YWTDISEPSI
1010 1020 1030 1040 1050
GRASLHGGEP TTIIRQDLGS PEGIALDHLG RTIFWTDSQL DRIEVAKMDG
1060 1070 1080 1090 1100
TQRRVLFDTG LVNPRGIVTD PVRGNLYWTD WNRDNPKIET SHMDGTNRRI
1110 1120 1130 1140 1150
LAQDNLGLPN GLTFDAFSSQ LCWVDAGTHR AECLNPAQPG RRKVLEGLQY
1160 1170 1180 1190 1200
PFAVTSYGKN LYYTDWKTNS VIAMDLAISK EMDTFHPHKQ TRLYGITIAL
1210 1220 1230 1240 1245
SQCPQGHNYC SVNNGGCTHL CLPTPGSRTC RCPDNTLGVD CIERK

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 non-CPTAC-3848 Collapse assay details

Data source: Panorama

Official Gene Symbol

Nid1

Peptide Sequence

YALSNSIGPVR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

649

Peptide End

659

CPTAC ID

non-CPTAC-3848

Peptide Molecular Mass

1,175.6299

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 R

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

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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 | | y9 (1+) | 8.1 | 5.1 | 5.7 | 11.2 | 8.8 | 7.9 | 13.8 | 10.2 | 9.7 | 15 | 15 | 15 | | y8 (1+) | 7.1 | 4.8 | 7.6 | 10.4 | 7.4 | 8.4 | 12.6 | 8.8 | 11.3 | 15 | 15 | 15 | | y4 (1+) | 10.3 | 4.9 | 5.9 | 12.1 | 7.9 | 7.7 | 15.9 | 9.3 | 9.7 | 15 | 15 | 15 | | y9 (2+) | 19.8 | 6.2 | 9.3 | 36 | 10.4 | 9 | 41.1 | 12.1 | 12.9 | 15 | 15 | 15 | | b2 (1+) | 7.7 | 3.3 | 3.7 | 8.5 | 8.3 | 7.3 | 11.5 | 8.9 | 8.2 | 15 | 15 | 15 | | sum | 3.6 | 1.1 | 3.5 | 8.8 | 7 | 5.5 | 9.5 | 7.1 | 6.5 | 15 | 15 | 15 |

Additional Resources and Comments