PDGFRB, CPTAC-1630 - CPTAC Assay Portal (original) (raw)

Please include the following statement when referencing the CPTAC Assay Portal

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.

PDGFRB

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

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-1630 Collapse assay details

Data source: Panorama

Official Gene Symbol

PDGFRB

Peptide Sequence

LLGEVGTLQFAELHR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

318

Peptide End

332

CPTAC ID

CPTAC-1630

Peptide Molecular Mass

1,681.9152

Species

Homo sapiens (Human)

Assay Type

Direct MRM or SRM

Matrix

Ovarian cancer tumor tissue lysate

Submitting Laboratory

Pacific Northwest National Laboratory

Submitting Lab PI

Tao Liu

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

TSQ Vantage

Internal Standard

peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Waters nanoACQUITY (Part Number 176016000)

Column Packing

Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)

Column Dimensions

100 um x 100 mm

Flow Rate

0.5 uL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y6 (1+) | 9.4 | 2.2 | 3.2 | 18.4 | 6.3 | 7.1 | 20.7 | 6.7 | 7.8 | 15 | 15 | 15 | | y8 (1+) | 12.4 | 4.4 | 4.5 | 16.3 | 6.2 | 5.7 | 20.5 | 7.6 | 7.3 | 15 | 15 | 15 | | y10 (1+) | 14.1 | 5.6 | 5.1 | 19.9 | 9.9 | 8.9 | 24.4 | 11.4 | 10.3 | 15 | 15 | 15 | | sum | 6.8 | 1.9 | 2.6 | 15.2 | 6.4 | 5.9 | 16.7 | 6.7 | 6.4 | 15 | 15 | 15 |

Additional Resources and Comments

Comments

Assay Details for CPTAC-3063 Collapse assay details

Data source: Panorama

Official Gene Symbol

PDGFRB

Peptide Modified Sequence

GGPIYIITEYC[+57.0]R

Modification Type

Carbamidomethyl (C)

Protein - Site of Modification

685

Peptide - Site of Modification

11

Peptide Start

674

Peptide End

685

CPTAC ID

CPTAC-3063

Peptide Molecular Mass

1,440.7071

Species

Homo Sapiens

Assay Type

Direct MRM or SRM

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

25 fmol on column

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Easy-nLC 1000 Thermo Scientific

Column Packing

C18

Column Dimensions

75 µm x 50 cm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y8 (1+) | 4 | 5 | 2.9 | 7.6 | 5.2 | 2.8 | 8.6 | 7.2 | 4 | 15 | 15 | 15 | | y6 (1+) | 2.9 | 5.2 | 2.8 | 6.1 | 5.2 | 3.1 | 6.8 | 7.4 | 4.2 | 15 | 15 | 15 | | y7 (1+) | 4.1 | 4.8 | 2.6 | 7.2 | 4.7 | 2.7 | 8.3 | 6.7 | 3.7 | 15 | 15 | 15 | | sum | 3.1 | 4.9 | 2.6 | 6.7 | 4.9 | 2.8 | 7.4 | 6.9 | 3.8 | 15 | 15 | 15 |

Additional Resources and Comments

Comments