Dld, CPTAC-3704 - 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-3704: View additional IDVSVEAASGGK data

CPTAC-2727: View additional ADGGTQVIDTK data

10 20 30 40 50
MQSWSRVYRS LAKKGHFNRI SHGLQGVSSV PLRTYADQPI EADVTVIGSG
60 70 80 90 100
PGGYVAAIKS AQLGFKTVCI EKNETLGGTC LNVGCIPSKA LLNNSHYYHM
110 120 130 140 150
AHGKDFASRG IEIPEVRLNL EKMMEQKHSA VKALTGGIAH LFKQNKVVHV
160 170 180 190 200
NGFGKITGKN QVTATKADGS TQVIDTKNIL VATGSEVTPF PGITIDEDTI
210 220 230 240 250
VSSTGALSLK KVPEKLVVIG AGVIGVELGS VWQRLGADVT AVEFLGHVGG
260 270 280 290 300
IGIDMEISKN FQRILQRQGF KFKLNTKVTG ATKKSDGKID VSVEAASGGK
310 320 330 340 350
AEVITCDVLL VCIGRRPFTQ NLGLEELGIE LDPKGRIPVN NRFQTKIPNI
360 370 380 390 400
YAIGDVVAGP MLAHKAEDEG IICVEGMAGG AVHIDYNCVP SVIYTHPEVA
410 420 430 440 450
WVGKSEEQLK EEGIEFKIGK FPFAANSRAK TNADTDGMVK ILGHKSTDRV
460 470 480 490 500
LGAHILGPGA GEMVNEAALA LEYGASCEDI ARVCHAHPTL SEAFREANLA
509
AAFGKPINF

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-3704 Collapse assay details

Data source: Panorama

Official Gene Symbol

Dld

Peptide Sequence

IDVSVEAASGGK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

289

Peptide End

300

CPTAC ID

non-CPTAC-3704

Peptide Molecular Mass

1,131.5772

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 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

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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+) | 11.2 | 6.1 | 5 | 12.3 | 7.8 | 5.7 | 16.6 | 9.9 | 7.6 | 15 | 15 | 15 | | y4 (1+) | 10.1 | 8.2 | 9.7 | 12.9 | 9 | 8 | 16.4 | 12.2 | 12.6 | 15 | 15 | 15 | | y7 (1+) | 10 | 6.2 | 4.2 | 9.9 | 6.3 | 7.8 | 14.1 | 8.8 | 8.9 | 15 | 15 | 15 | | y9 (1+) | 13.3 | 4.9 | 6.3 | 14 | 7.7 | 8.6 | 19.3 | 9.1 | 10.7 | 15 | 15 | 15 | | y10 (1+) | 7.3 | 5.7 | 4.9 | 9 | 6.4 | 9.1 | 11.6 | 8.6 | 10.3 | 15 | 15 | 15 | | sum | 4.2 | 2.2 | 3 | 6.1 | 4.2 | 6.2 | 7.4 | 4.7 | 6.9 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-2727 Collapse assay details

Data source: Panorama

Official Gene Symbol

DLD

Peptide Sequence

ADGGTQVIDTK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

167

Peptide End

177

CPTAC ID

CPTAC-2727

Peptide Molecular Mass

1,103.5459

Species

Homo Sapiens

Assay Type

Direct MRM

Matrix

Tumor Digest

Submitting Laboratory

Washington University in St. Louis

Submitting Lab PI

Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

ThermoFisher Q-Exactive

Internal Standard

13 fmol on column

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Easy-nLC 1000 Thermo Scientific

Column Packing

C18

Column Dimensions

75 um x 50 cm

Flow Rate

300 nL/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 | | b3 (1+) | 13.3 | 7.8 | 32.7 | 13.5 | 7.5 | 44.5 | 19 | 10.8 | 55.2 | 15 | 15 | 15 | | y3 (1+) | 5.4 | 2.6 | 38.7 | 5.5 | 3.5 | 73.4 | 7.7 | 4.4 | 83 | 15 | 15 | 15 | | y4 (1+) | 5 | 2.4 | 34.4 | 6.3 | 2.6 | 54.8 | 8 | 3.5 | 64.7 | 15 | 15 | 15 | | sum | 4 | 2.7 | 19.1 | 4.8 | 3 | 21.6 | 6.2 | 4 | 28.8 | 15 | 15 | 15 |

Additional Resources and Comments