Making proteomics data accessible and reusable: current state of proteomics databases and repositories (Q28648439)

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13 March 2020

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25 November 2020

Making proteomics data accessible and reusable: current state of proteomics databases and repositories (English)

1 reference

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13 March 2020

Juan Antonio Vizcaíno

5

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13 March 2020

Yasset Perez-Riverol

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1 reference

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13 March 2020

Emanuele Alpi

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1 reference

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13 March 2020

author name string

Rui Wang

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13 March 2020

language of work or name

English

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publication date

1 March 2015

2 references

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13 March 2020

25 November 2020

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13 March 2020

25 November 2020

15

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13 March 2020

issue

5-6

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13 March 2020

page(s)

930-949

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Creative Commons Attribution 4.0 International

13 March 2020

copyright license

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describes a project that uses

25 November 2020

copyright status

copyrighted

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Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

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Status of large-scale analysis of post-translational modifications by mass spectrometry

17 March 2017

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Integration of cardiac proteome biology and medicine by a specialized knowledgebase

17 March 2017

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The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

17 March 2017

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Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

17 March 2017

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Corrigendum: Global quantification of mammalian gene expression control

17 March 2017

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neXtProt: organizing protein knowledge in the context of human proteome projects

17 March 2017

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The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

17 March 2017

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The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

17 March 2017

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PRIDE: quality control in a proteomics data repository

17 March 2017

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The mzIdentML data standard for mass spectrometry-based proteomics results

17 March 2017

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PRIDE Inspector: a tool to visualize and validate MS proteomics data

17 March 2017

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MOPED: Model Organism Protein Expression Database

17 March 2017

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PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

17 March 2017

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The BioSample Database (BioSD) at the European Bioinformatics Institute

17 March 2017

1 reference

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Published and perished? The influence of the searched protein database on the long-term storage of proteomics data

17 March 2017

1 reference

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Global quantification of mammalian gene expression control

17 March 2017

1 reference

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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

17 March 2017

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Iridovirus and microsporidian linked to honey bee colony decline

17 March 2017

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mzML--a community standard for mass spectrometry data

17 March 2017

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GeneCards Version 3: the human gene integrator

17 March 2017

1 reference

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Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research

17 March 2017

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The Ontology Lookup Service: bigger and better

17 March 2017

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Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry

17 March 2017

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Reanalysis of Tyrannosaurus rex Mass Spectra

17 March 2017

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Human Proteinpedia: a unified discovery resource for proteomics research

17 March 2017

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Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry

17 March 2017

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Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

17 March 2017

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

17 March 2017

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A statistical model for identifying proteins by tandem mass spectrometry

17 March 2017

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

17 March 2017

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Gene ontology: tool for the unification of biology

17 March 2017

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

17 March 2017

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KEGG: kyoto encyclopedia of genes and genomes

17 March 2017

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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

17 March 2017

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Human Protein Reference Database--2009 update

7 April 2017

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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

7 April 2017

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Andromeda: a peptide search engine integrated into the MaxQuant environment

7 April 2017

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Universal sample preparation method for proteome analysis

7 April 2017

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TANDEM: matching proteins with tandem mass spectra

7 April 2017

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Mass-spectrometry-based draft of the human proteome

7 April 2017

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A draft map of the human proteome

7 April 2017

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Activities at the Universal Protein Resource (UniProt)

7 April 2017

1 reference

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Update on activities at the Universal Protein Resource (UniProt) in 2013

7 April 2017

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A travel guide to Cytoscape plugins

7 April 2017

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How to submit MS proteomics data to ProteomeXchange via the PRIDE database

7 April 2017

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SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data

3 June 2018

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The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics

3 June 2018

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Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins

3 June 2018

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MOPED enables discoveries through consistently processed proteomics data

3 June 2018

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Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

3 June 2018

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State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project

3 June 2018

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An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays

3 June 2018

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Proteogenomic database construction driven from large scale RNA-seq data

3 June 2018

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Resilience in the proteomics data ecosystem: how the field cares for its data

3 June 2018

1 reference

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From Peptidome to PRIDE: public proteomics data migration at a large scale

3 June 2018

1 reference

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Access guide to human proteinpedia.

3 June 2018

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Controlled vocabularies and ontologies in proteomics: overview, principles and practice

3 June 2018

1 reference

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PRIDE Cluster: building a consensus of proteomics data

3 June 2018

1 reference

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The state of the human proteome in 2012 as viewed through PeptideAtlas

3 June 2018

1 reference

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Next-generation proteomics: towards an integrative view of proteome dynamics.

3 June 2018

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Current algorithmic solutions for peptide-based proteomics data generation and identification

3 June 2018

1 reference

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Mass spectrometry-based quantification

3 June 2018

1 reference

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Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites

3 June 2018

1 reference

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Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data

3 June 2018

1 reference

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MRMaid 2.0: mining PRIDE for evidence-based SRM transitions

3 June 2018

1 reference

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Shotgun protein sequencing with meta-contig assembly

3 June 2018

1 reference

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pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool

3 June 2018

1 reference

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PaxDb, a database of protein abundance averages across all three domains of life

3 June 2018

1 reference

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PASSEL: the PeptideAtlas SRMexperiment library

3 June 2018

1 reference

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Analysis of high accuracy, quantitative proteomics data in the MaxQB database

3 June 2018

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Fast multi-blind modification search through tandem mass spectrometry

3 June 2018

1 reference

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TraML--a standard format for exchange of selected reaction monitoring transition lists

3 June 2018

1 reference

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Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.

3 June 2018

1 reference

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The quantitative proteome of a human cell line.

3 June 2018

1 reference

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Deep proteome and transcriptome mapping of a human cancer cell line

3 June 2018

1 reference

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Protein identification using top-down.

3 June 2018

1 reference

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Algorithms for the de novo sequencing of peptides from tandem mass spectra

3 June 2018

1 reference

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Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

3 June 2018

1 reference

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Peptide identification by database search of mixture tandem mass spectra

3 June 2018

1 reference

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Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

SPIRE: Systematic protein investigative research environment

3 June 2018

1 reference

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A posteriori quality control for the curation and reuse of public proteomics data

3 June 2018

1 reference

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Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

3 June 2018

1 reference

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

compomics-utilities: an open-source Java library for computational 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=4409848

Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Building and searching tandem mass (MS/MS) 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=4409848

pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Less label, more free: approaches in label-free quantitative mass spectrometry.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Proteomics databases and repositories

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Tranche distributed repository and ProteomeCommons.org

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Peptide identification from mixture tandem mass spectra

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

A guided tour of the Trans-Proteomic 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=4409848

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Proteomics data repositories

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

False discovery rates of protein identifications: a strike against the two-peptide rule

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

NCBI Peptidome: a new public repository for mass spectrometry peptide identifications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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=4409848

Discovery and revision of Arabidopsis genes by proteogenomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

A database of mass spectrometric assays for the yeast proteome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Spectral probabilities and generating functions of tandem mass spectra: a strike against 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=4409848

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=4409848

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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=4409848

Interpreting sequences from mastodon and T. rex.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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=4409848

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

A human protein atlas for normal and cancer tissues based on antibody 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=4409848

The use of proteotypic peptide 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=4409848

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=4409848

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=4409848

Guidelines for human gene nomenclature

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Analyzing the first drafts of the human proteome.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Towards a human proteomics atlas

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Bromenshenk et al (PLoS One, 2011, 5(10):e13181) have claimed to have found peptides from an invertebrate iridovirus in bees

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Peptide fractionation by acid pH SDS-free electrophoresis

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Peptide identification quality control

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Using the Human Plasma PeptideAtlas to study human plasma proteins

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Reactome knowledgebase of human biological pathways and processes.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Proteomics based on peptide fractionation by SDS-free PAGE.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

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=4409848

PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

Computational prediction of proteotypic peptides for quantitative proteomics.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409848

A home for raw proteomics data

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25158685

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Credit where credit is overdue

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25158685

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PMIC.201400302

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158685%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158685%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158685%20AND%20SRC:MED&resulttype=core&format=json