(Q50995899)

26 March 2018

case report

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title

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). (English)

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26 March 2018

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3

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Henning Hermjakob

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Gil Omenn

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Peipei Ping

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Richard Simpson

29

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Richard D. Smith

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David Tabb

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Eric W Deutsch

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Eric W Deutsch

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Robert L Moritz

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Henry Daniel Ponce-Rodríguez

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Henry Rodriguez

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Christoph H Borchers

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Christoph H Borchers

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Patrik Kolar

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Patrik Kolar

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Richard S. Stein

32

Stephen E Stein

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Christopher R Kinsinger

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Christopher R Kinsinger

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James Apffel

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James Apffel

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Xiaopeng Bian

4

Xiaopeng Bian

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Mi-Youn Brusniak

7

Mi-Youn Brusniak

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Bruno Domon

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Bruno Domon

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Rudolf Grimm

12

Rudolf Grimm

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Hanno Langen

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Hanno Langen

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Ron Orlando

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Ron Orlando

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Douglas Slotta

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Douglas Slotta

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Danilo A Tagle

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Danilo Tagle

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26 March 2018

author name string

Ralph Bradshaw

6

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Daniel W Chan

8

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Jeff Gorman

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William Hancock

13

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David Horn

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Christie Hunter

16

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Hans-Joachim Kraus

18

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Rune Linding

20

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Akhilesh Pandey

24

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Amir Rahbar

26

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Robert Rivers

27

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Sean L Seymour

28

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John R Yates

35

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26 March 2018

publication date

3 November 2011

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26 March 2018

Molecular & Cellular Proteomics

published in

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26 March 2018

volume

10

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issue

12

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26 March 2018

page(s)

O111.015446

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26 March 2018

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

mProphet: automated data processing and statistical validation for large-scale SRM experiments

22 May 2018

1 reference

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mzML--a community standard for mass spectrometry data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Evolution of clinical proteomics and its role in medicine

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The Proteomics Identifications database: 2010 update

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Statistical calibration of the SEQUEST XCorr function

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

mzML: a single, unifying data format for mass spectrometer output

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Proteomics FASTA archive and reference resource

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The minimum information about a proteomics experiment (MIAPE)

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Validated MALDI-TOF/TOF mass spectra for protein standards

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Automatic validation of phosphopeptide identifications from tandem mass spectra

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Guidelines for the next 10 years of proteomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Open source system for analyzing, validating, and storing protein identification data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The Human Proteome Organization Plasma Proteome Project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

A statistical model for identifying proteins by tandem mass spectrometry

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The human proteome project: Current state and future direction.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Census for proteome quantification

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

Reporting protein identification data: the next generation of guidelines.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3237091

The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation

14 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22052993

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Revised draft guidelines for proteomic data publication

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22052993

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1074/MCP.O111.015446

1 reference

26 March 2018

PMC publication ID

3237091

1 reference

26 March 2018

PubMed publication ID

22052993

1 reference

26 March 2018