A guide to the Proteomics Identifications Database proteomics data repository (Q28748628)

3

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Juan Antonio Vizcaíno

1

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Lennart Martens

object named as

Lennart Martens

8

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Rick H. Cote

2

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Richard Côté

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Jonathan Rameseder

6

object named as

Jonathan Rameseder

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author name string

Joseph M Foster

4

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Michael Mueller

Human Proteinpedia: a unified discovery resource for proteomics research

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publication date

September 2009

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language of work or name

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9

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issue

18

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page(s)

4276-83

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cites work

1 reference

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16 March 2017

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PRIDE: new developments and new datasets

16 March 2017

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The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

16 March 2017

1 reference

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An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ

16 March 2017

1 reference

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The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

16 March 2017

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

16 March 2017

1 reference

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A common open representation of mass spectrometry data and its application to proteomics research

16 March 2017

1 reference

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Open mass spectrometry search algorithm

16 March 2017

1 reference

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

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

16 March 2017

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NCBI Reference Sequences: current status, policy and new initiatives

7 April 2017

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The minimum information about a proteomics experiment (MIAPE)

7 April 2017

1 reference

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The International Protein Index: an integrated database for proteomics experiments

7 April 2017

1 reference

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TANDEM: matching proteins with tandem mass spectra

7 April 2017

1 reference

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BioMart--biological queries made easy

7 April 2017

1 reference

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Reactome knowledgebase of human biological pathways and processes

7 April 2017

1 reference

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FlyBase: enhancing Drosophila Gene Ontology annotations

7 April 2017

1 reference

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The Universal Protein Resource (UniProt) 2009

7 April 2017

1 reference

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IntAct--open source resource for molecular interaction data

7 April 2017

1 reference

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Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

7 April 2017

1 reference

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PRIDE Converter: making proteomics data-sharing easy

9 May 2017

1 reference

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Recent developments in public proteomic MS repositories and pipelines.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

A suite of tools to analyse and publish 2-DE data.

3 June 2018

1 reference

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MAPU 2.0: high-accuracy proteomes mapped to genomes

3 June 2018

1 reference

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PepSeeker: mining information from proteomic 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=2970915

The PRIDE proteomics identifications database: data submission, query, and dataset comparison

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

Analyzing large-scale proteomics projects with latent semantic indexing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

Genome browsing with Ensembl: a practical overview.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition

3 June 2018

1 reference

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Public proteomic MS repositories and pipelines: available tools and biological applications.

3 June 2018

1 reference

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MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS 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=2970915

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=2970915

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

PRIDE: the proteomics identifications database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

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=2970915

The RESID Database of Protein Modifications as a resource and annotation tool

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

The Protein Data Bank: a historical perspective

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPMIC.200900402

Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

Unimod: Protein modifications for mass spectrometry

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

The need for a public proteomics repository

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970915

GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19662629

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Democratizing proteomics data

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19662629