The mzIdentML data standard for mass spectrometry-based proteomics results (Q28727227)

4

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Juan Antonio Vizcaíno

17

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Johannes Griss

16

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Gerhard Mayer

Gerhard Mayer

3

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Julian N Selley

Julian N Selley

7

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Angel Pizarro

Angel Pizarro

19

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Pierre-Alain Binz

Pierre-Alain Binz

12

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Andrew Jones

Andrew R Jones

1

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Simon J. Hubbard

Simon J Hubbard

6

0 references

Eric W Deutsch

13

Eric W Deutsch

0 references

Martin Eisenacher

2

Martin Eisenacher

0 references

Florian Reisinger

15

Florian Reisinger

0 references

James Shofstahl

9

James Shofstahl

0 references

author name string

Jennifer Siepen

5

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Brian C Searle

8

0 references

Sean L Seymour

10

0 references

Randall Julian

11

0 references

Matthew Chambers

18

0 references

David Creasy

Molecular & Cellular Proteomics

20

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publication date

July 2012

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language of work or name

English

0 references

published in

0 references

volume

11

0 references

issue

7

0 references

page(s)

M111.014381

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cites work

mzML--a community standard for mass spectrometry data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

OpenMS - an open-source software framework for mass spectrometry

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

PRIDE: a public repository of protein and peptide identifications for the proteomics community

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

17 March 2017

The PeptideAtlas project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Open mass spectrometry search algorithm

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

A statistical model for identifying proteins by tandem mass spectrometry

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

OLAV: towards high-throughput tandem mass spectrometry data identification

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Probability-based protein identification by searching sequence databases using mass spectrometry data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Error-tolerant identification of peptides in sequence databases by peptide sequence tags

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

The minimum information about a proteomics experiment (MIAPE)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

A community standard format for the representation of protein affinity reagents

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Building consensus spectral libraries for peptide identification in proteomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

ProteoWizard: open source software for rapid proteomics tools development

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Using BiblioSpec for creating and searching tandem MS peptide libraries

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

The minimum information required for reporting a molecular interaction experiment (MIMIx).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

The PSI formal document process and its implementation on the PSI website

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

TOPP--the OpenMS proteomics pipeline

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Using annotated peptide mass spectrum libraries for protein identification

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

PepNovo: de novo peptide sequencing via probabilistic network modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Probability-based validation of protein identifications using a modified SEQUEST algorithm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

ProFound: an expert system for protein identification using mass spectrometric peptide mapping information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry

3 June 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Unimod: Protein modifications for mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

The PSI-MOD community standard for representation of protein modification data

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Guidelines for reporting the use of mass spectrometry informatics in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Guidelines for reporting the use of gel electrophoresis in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Guidelines for reporting the use of mass spectrometry in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Reporting protein identification data: the next generation of guidelines

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4–6, 2005

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014381

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394945

Credit where credit is overdue

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22375074