RPS6, CPTAC-1331 - 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

10 20 30 40 50
MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV
60 70 80 90 100
RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRTG ERKRKSVRGC
110 120 130 140 150
IVDANLSVLN LVIVKKGEKD IPGLTDTTVP RRLGPKRASR IRKLFNLSKE
160 170 180 190 200
DDVRQYVVRK PLNKEGKKPR TKAPKIQRLV TPRVLQHKRR RIALKKQRTK
210 220 230 240 249
KNKEEAAEYA KLLAKRMKEA KEKRQEQIAK RRRLSSLRAS TSKSESSQK

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-1331 Collapse assay details

Data source: Panorama

Official Gene Symbol

RPS6

Peptide Modified Sequence

LS[+80.0]SLRASTSK

Modification Type

Phospho (ST)

Protein - Site of Modification

235

Peptide - Site of Modification

2

Peptide Start

234

Peptide End

243

CPTAC ID

CPTAC-1331

Peptide Molecular Mass

1,128.5540

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

Fe(III)-NTA

Matrix

Digested Cell Lysate

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr

Publication

View Details (opens in a new window)

Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

medium stable isotope peptide (delta 6 amu)

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 3 um, 200A

Column Dimensions

0.075 x 100 mm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Broad Institute-Biologist curated set of targets across a number of important cancer pathways

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 | | y8 (1+) | 18.1 | 15.8 | 14.5 | 20.4 | 13.9 | 12.4 | 27.3 | 21 | 19.1 | 15 | 15 | 15 | | sum | 18.1 | 15.8 | 14.5 | 20.4 | 13.9 | 12.4 | 27.3 | 21 | 19.1 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-1332 Collapse assay details

Data source: Panorama

Official Gene Symbol

RPS6

Peptide Modified Sequence

LSS[+80.0]LRASTSK

Modification Type

Phospho (ST)

Protein - Site of Modification

236

Peptide - Site of Modification

3

Peptide Start

234

Peptide End

243

CPTAC ID

CPTAC-1332

Peptide Molecular Mass

1,128.5540

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

Fe(III)-NTA

Matrix

Digested Cell Lysate

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr

Publication

View Details (opens in a new window)

Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

medium stable isotope peptide (delta 6 amu)

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 3 um, 200A

Column Dimensions

0.075 x 100 mm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Broad Institute-Biologist curated set of targets across a number of important cancer pathways

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 | | y8 (1+) | 18.5 | 14.9 | 14.6 | 23.2 | 17.4 | 19.1 | 29.7 | 22.9 | 24 | 15 | 15 | 15 | | sum | 18.5 | 14.9 | 14.6 | 23.2 | 17.4 | 19.1 | 29.7 | 22.9 | 24 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-1333 Collapse assay details

Data source: Panorama

Official Gene Symbol

RPS6

Peptide Modified Sequence

LSSLRAS[+80.0]TSK

Modification Type

Phospho (ST)

Protein - Site of Modification

240

Peptide - Site of Modification

7

Peptide Start

234

Peptide End

243

CPTAC ID

CPTAC-1333

Peptide Molecular Mass

1,128.5540

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

Fe(III)-NTA

Matrix

Digested Cell Lysate

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr

Publication

View Details (opens in a new window)

Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

medium stable isotope peptide (delta 6 amu)

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 3 um, 200A

Column Dimensions

0.075 x 100 mm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Broad Institute-Biologist curated set of targets across a number of important cancer pathways

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 | | b5 (1+) | 14 | 13 | 14.8 | 15.3 | 19.9 | 16.6 | 20.7 | 23.8 | 22.2 | 15 | 15 | 15 | | y7 (1+) | 52.8 | 50.1 | 56.9 | 66 | 66.3 | 66.3 | 84.5 | 83.1 | 87.4 | 15 | 15 | 15 | | b9-98 (1+) | 23.5 | 16.7 | 12.3 | 26.8 | 19.2 | 15.8 | 35.6 | 25.4 | 20 | 15 | 15 | 15 | | sum | 11.5 | 11.1 | 9.9 | 11.6 | 15 | 12.4 | 16.3 | 18.7 | 15.9 | 15 | 15 | 15 |

Additional Resources and Comments