Grin2a, CPTAC-3341 - 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-3341: View additional FSYIPEAK data

10 20 30 40 50
MGRLGYWTLL VLPALLVWHG PAQNAAAEKG TPALNIAVLL GHSHDVTERE
60 70 80 90 100
LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDLM SGARIHGLVF
110 120 130 140 150
GDDTDQEAVA QMLDFISSQT FIPILGIHGG ASMIMADKDP TSTFFQFGAS
160 170 180 190 200
IQQQATVMLK IMQDYDWHVF SLVTTIFPGY RDFISFIKTT VDNSFVGWDM
210 220 230 240 250
QNVITLDTSF EDAKTQVQLK KIHSSVILLY CSKDEAVLIL SEARSLGLTG
260 270 280 290 300
YDFFWIVPSL VSGNTELIPK EFPSGLISVS YDDWDYSLEA RVRDGLGILT
310 320 330 340 350
TAASSMLEKF SYIPEAKASC YGQTEKPETP LHTLHQFMVN VTWDGKDLSF
360 370 380 390 400
TEEGYQVHPR LVVIVLNKDR EWEKVGKWEN QTLSLRHAVW PRYKSFSDCE
410 420 430 440 450
PDDNHLSIVT LEEAPFVIVE DIDPLTETCV RNTVPCRKFV KINNSTNEGM
460 470 480 490 500
NVKKCCKGFC IDILKKLSRT VKFTYDLYLV TNGKHGKKVN NVWNGMIGEV
510 520 530 540 550
VYQRAVMAVG SLTINEERSE VVDFSVPFVE TGISVMVSRS NGTVSPSAFL
560 570 580 590 600
EPFSASVWVM MFVMLLIVSA IAVFVFEYFS PVGYNRNLAK GKAPHGPSFT
610 620 630 640 650
IGKAIWLLWG LVFNNSVPVQ NPKGTTSKIM VSVWAFFAVI FLASYTANLA
660 670 680 690 700
AFMIQEEFVD QVTGLSDKKF QRPHDYSPPF RFGTVPNGST ERNIRNNYPY
710 720 730 740 750
MHQYMTKFNQ RGVEDALVSL KTGKLDAFIY DAAVLNYKAG RDEGCKLVTI
760 770 780 790 800
GSGYIFATTG YGIALQKGSP WKRQIDLALL QFVGDGEMEE LETLWLTGIC
810 820 830 840 850
HNEKNEVMSS QLDIDNMAGV FYMLAAAMAL SLITFIWEHL FYWKLRFCFT
860 870 880 890 900
GVCSDRPGLL FSISRGIYSC IHGVHIEEKK KSPDFNLTGS QSNMLKLLRS
910 920 930 940 950
AKNISNMSNM NSSRMDSPKR AADFIQRGSL IVDMVSDKGN LIYSDNRSFQ
960 970 980 990 1000
GKDSIFGENM NELQTFVANR HKDSLSNYVF QGQHPLTLNE SNPNTVEVAV
1010 1020 1030 1040 1050
STESKGNSRP RQLWKKSMES LRQDSLNQNP VSQRDEKTAE NRTHSLKSPR
1060 1070 1080 1090 1100
YLPEEVAHSD ISETSSRATC HREPDNNKNH KTKDNFKRSM ASKYPKDCSE
1110 1120 1130 1140 1150
VERTYVKTKA SSPRDKIYTI DGEKEPSFHL DPPQFIENIV LPENVDFPDT
1160 1170 1180 1190 1200
YQDHNENFRK GDSTLPMNRN PLHNEDGLPN NDQYKLYAKH FTLKDKGSPH
1210 1220 1230 1240 1250
SEGSDRYRQN STHCRSCLSN LPTYSGHFTM RSPFKCDACL RMGNLYDIDE
1260 1270 1280 1290 1300
DQMLQETGNP ATREEAYQQD WSQNNALQFQ KNKLKINRQH SYDNILDKPR
1310 1320 1330 1340 1350
EIDLSRPSRS ISLKDRERLL EGNLYGSLFS VPSSKLLGNK SSLFPQGLED
1360 1370 1380 1390 1400
SKRSKSLLPD HTSDNPFLHT YGDDQRLVIG RCPSDPYKHS LPSQAVNDSY
1410 1420 1430 1440 1450
LRSSLRSTAS YCSRDSRGHS DVYISEHVMP YAANKNNMYS TPRVLNSCSN
1460 1464
RRVYKKMPSI ESDV

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-3342 Collapse assay details

Data source: Panorama

Official Gene Symbol

Grin2a

Peptide Sequence

DLSFTEEGYQVHPR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

347

Peptide End

360

CPTAC ID

non-CPTAC-3342

Peptide Molecular Mass

1,676.7795

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 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 | | b2 (1+) | 4.4 | 5.5 | 4.3 | 15.1 | 12.2 | 5.9 | 15.7 | 13.4 | 7.3 | 15 | 15 | 15 | | y10 (2+) | 4.5 | 8 | 5.4 | 16.5 | 11.7 | 5.8 | 17.1 | 14.2 | 7.9 | 15 | 15 | 15 | | y11 (2+) | 7.1 | 9.2 | 6.9 | 11 | 9 | 7.5 | 13.1 | 12.9 | 10.2 | 15 | 15 | 15 | | y12 (2+) | 5.6 | 5.9 | 6.2 | 16.5 | 10.8 | 6.1 | 17.4 | 12.3 | 8.7 | 15 | 15 | 15 | | y2 (1+) | 3.6 | 5.7 | 7.6 | 17.4 | 18.5 | 5.7 | 17.8 | 19.4 | 9.5 | 15 | 15 | 15 | | sum | 2.2 | 3.8 | 3.1 | 15.3 | 10.6 | 3.7 | 15.5 | 11.3 | 4.8 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3341 Collapse assay details

Data source: Panorama

Official Gene Symbol

Grin2a

Peptide Sequence

FSYIPEAK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

310

Peptide End

317

CPTAC ID

non-CPTAC-3341

Peptide Molecular Mass

953.4858

Species

Mus musculus (Mouse)

Assay Type

Direct MRM

Matrix

Plasma

Submitting Laboratory

UVic-Genome BC Proteomics Centre

Submitting Lab PI

Christoph Borchers

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

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 | | b2 (1+) | 8.6 | 7.8 | 11.1 | 19.8 | 13 | 13.2 | 21.6 | 15.2 | 17.2 | 15 | 15 | 15 | | y4 (1+) | 15.4 | 10.6 | 15.1 | 21.9 | 11.1 | 12.2 | 26.8 | 15.3 | 19.4 | 15 | 15 | 15 | | y5 (1+) | 14.2 | 9.9 | 9.8 | 17.3 | 10 | 9.2 | 22.4 | 14.1 | 13.4 | 15 | 15 | 15 | | y6 (1+) | 9.4 | 8.1 | 14.2 | 13 | 8.1 | 12.3 | 16 | 11.5 | 18.8 | 15 | 15 | 15 | | y7 (1+) | 11 | 12.9 | 15.5 | 23.2 | 22.6 | 16.1 | 25.7 | 26 | 22.3 | 15 | 15 | 15 | | sum | 4.5 | 4.5 | 7.9 | 15.5 | 10.1 | 7.5 | 16.1 | 11.1 | 10.9 | 15 | 15 | 15 |

Additional Resources and Comments