Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
Authors
Keywords
-
Journal
PROTEOMICS
Volume 15, Issue 5-6, Pages 930-950
Publisher
Wiley
Online
2014-08-27
DOI
10.1002/pmic.201400302
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Analyzing the First Drafts of the Human Proteome
- (2014) Iakes Ezkurdia et al. JOURNAL OF PROTEOME RESEARCH
- PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments
- (2014) Yassene Mohammed et al. Journal of Proteomics
- SpliceVista, a Tool for Splice Variant Identification and Visualization in Shotgun Proteomics Data
- (2014) Yafeng Zhu et al. MOLECULAR & CELLULAR PROTEOMICS
- A draft map of the human proteome
- (2014) Min-Sik Kim et al. NATURE
- Mass-spectrometry-based draft of the human proteome
- (2014) Mathias Wilhelm et al. NATURE
- ProteomeXchange provides globally coordinated proteomics data submission and dissemination
- (2014) Juan A Vizcaíno et al. NATURE BIOTECHNOLOGY
- The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics
- (2014) Francesco Lanucara et al. Nature Chemistry
- MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data
- (2014) Elizabeth Montague et al. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
- How to submit MS proteomics data to ProteomeXchange via the PRIDE database
- (2014) Tobias Ternent et al. PROTEOMICS
- Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
- (2013) Gerhard Mayer et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
- (2013) Yasset Perez-Riverol et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Integration of Cardiac Proteome Biology and Medicine by a Specialized Knowledgebase
- (2013) Nobel C. Zong et al. CIRCULATION RESEARCH
- 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
- (2013) Terry Farrah et al. JOURNAL OF PROTEOME RESEARCH
- Metrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins
- (2013) Lydie Lane et al. JOURNAL OF PROTEOME RESEARCH
- MOPED Enables Discoveries through Consistently Processed Proteomics Data
- (2013) Roger Higdon et al. JOURNAL OF PROTEOME RESEARCH
- Proteogenomic Database Construction Driven from Large Scale RNA-seq Data
- (2013) Sunghee Woo et al. JOURNAL OF PROTEOME RESEARCH
- Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
- (2013) Yasset Perez-Riverol et al. Journal of Proteomics
- SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping
- (2013) Lázaro H. Betancourt et al. Journal of Proteomics
- Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry
- (2013) Jesper V. Olsen et al. MOLECULAR & CELLULAR PROTEOMICS
- The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics
- (2013) Mathias Walzer et al. MOLECULAR & CELLULAR PROTEOMICS
- An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays
- (2013) Natalie E. Castellana et al. MOLECULAR & CELLULAR PROTEOMICS
- Erratum: Corrigendum: Global quantification of mammalian gene expression control
- (2013) Björn Schwanhäusser et al. NATURE
- PRIDE Cluster: building a consensus of proteomics data
- (2013) Johannes Griss et al. NATURE METHODS
- HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
- (2013) Rui M M Branca et al. NATURE METHODS
- Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
- (2013) Ute Distler et al. NATURE METHODS
- Activities at the Universal Protein Resource (UniProt)
- (2013) NUCLEIC ACIDS RESEARCH
- Ensembl 2014
- (2013) Paul Flicek et al. NUCLEIC ACIDS RESEARCH
- Resilience in the proteomics data ecosystem: How the field cares for its data
- (2013) Lennart Martens PROTEOMICS
- From Peptidome to PRIDE: Public proteomics data migration at a large scale
- (2013) Attila Csordas et al. PROTEOMICS
- Towards a human proteomics atlas
- (2012) Giulia Gonnelli et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Mass spectrometry-based quantification
- (2012) Leroi V. DeSouza et al. CLINICAL BIOCHEMISTRY
- Current algorithmic solutions for peptide-based proteomics data generation and identification
- (2012) Michael R Hoopmann et al. CURRENT OPINION IN BIOTECHNOLOGY
- The State of the Human Proteome in 2012 as Viewed through PeptideAtlas
- (2012) Terry Farrah et al. JOURNAL OF PROTEOME RESEARCH
- neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
- (2012) Pascale Gaudet et al. JOURNAL OF PROTEOME RESEARCH
- Discovery ofO-GlcNAc-6-phosphate Modified Proteins in Large-scale Phosphoproteomics Data
- (2012) Hannes Hahne et al. MOLECULAR & CELLULAR PROTEOMICS
- The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
- (2012) Richard G. Côté et al. MOLECULAR & CELLULAR PROTEOMICS
- Letter to Editor
- (2012) Leonard J. Foster MOLECULAR & CELLULAR PROTEOMICS
- Shotgun Protein Sequencing with Meta-contig Assembly
- (2012) Adrian Guthals et al. MOLECULAR & CELLULAR PROTEOMICS
- Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database
- (2012) Christoph Schaab et al. MOLECULAR & CELLULAR PROTEOMICS
- The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
- (2012) Andrew R. Jones et al. MOLECULAR & CELLULAR PROTEOMICS
- PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life
- (2012) M. Wang et al. MOLECULAR & CELLULAR PROTEOMICS
- PRIDE Inspector: a tool to visualize and validate MS proteomics data
- (2012) Rui Wang et al. NATURE BIOTECHNOLOGY
- The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome
- (2012) Young-Ki Paik et al. NATURE BIOTECHNOLOGY
- A home for raw proteomics data
- (2012) NATURE METHODS
- Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites
- (2012) Ivan Matic et al. NATURE METHODS
- A travel guide to Cytoscape plugins
- (2012) Rintaro Saito et al. NATURE METHODS
- Next-generation proteomics: towards an integrative view of proteome dynamics
- (2012) A. F. Maarten Altelaar et al. NATURE REVIEWS GENETICS
- The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
- (2012) Juan Antonio Vizcaíno et al. NUCLEIC ACIDS RESEARCH
- Update on activities at the Universal Protein Resource (UniProt) in 2013
- (2012) NUCLEIC ACIDS RESEARCH
- MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions
- (2012) Jun Fan et al. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
- PASSEL: The PeptideAtlas SRMexperiment library
- (2012) Terry Farrah et al. PROTEOMICS
- PRIDE: Quality control in a proteomics data repository
- (2012) A. Csordas et al. Database-The Journal of Biological Databases and Curation
- pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool
- (2012) Matthias Hirsch-Hoffmann et al. Frontiers in Plant Science
- ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
- (2011) Mi-Youn K Brusniak et al. BMC BIOINFORMATICS
- compomics-utilities: an open-source Java library for computational proteomics
- (2011) Harald Barsnes et al. BMC BIOINFORMATICS
- Peptide fractionation by acid pH SDS-free electrophoresis
- (2011) Yassel Ramos et al. ELECTROPHORESIS
- Algorithms for thede novosequencing of peptides from tandem mass spectra
- (2011) Jens Allmer Expert Review of Proteomics
- Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
- (2011) M. Brosch et al. GENOME RESEARCH
- pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana
- (2011) Katja Baerenfaller et al. Integrative Biology
- Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
- (2011) Jürgen Cox et al. JOURNAL OF PROTEOME RESEARCH
- SPIRE: Systematic protein investigative research environment
- (2011) Eugene Kolker et al. Journal of Proteomics
- Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
- (2011) Henry Lam et al. METHODS
- Fast Multi-blind Modification Search through Tandem Mass Spectrometry
- (2011) Seungjin Na et al. MOLECULAR & CELLULAR PROTEOMICS
- Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer
- (2011) Annette Michalski et al. MOLECULAR & CELLULAR PROTEOMICS
- Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data
- (2011) Johannes Griss et al. MOLECULAR & CELLULAR PROTEOMICS
- Protein Identification Using Top-Down Spectra
- (2011) Xiaowen Liu et al. MOLECULAR & CELLULAR PROTEOMICS
- Peptide Identification by Database Search of Mixture Tandem Mass Spectra
- (2011) Jian Wang et al. MOLECULAR & CELLULAR PROTEOMICS
- TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
- (2011) Eric W. Deutsch et al. MOLECULAR & CELLULAR PROTEOMICS
- Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis
- (2011) Renu Goel et al. Molecular BioSystems
- Deep proteome and transcriptome mapping of a human cancer cell line
- (2011) N. Nagaraj et al. Molecular Systems Biology
- The quantitative proteome of a human cell line
- (2011) M. Beck et al. Molecular Systems Biology
- Global quantification of mammalian gene expression control
- (2011) Björn Schwanhäusser et al. NATURE
- mProphet: automated data processing and statistical validation for large-scale SRM experiments
- (2011) Lukas Reiter et al. NATURE METHODS
- The BioSample Database (BioSD) at the European Bioinformatics Institute
- (2011) M. Gostev et al. NUCLEIC ACIDS RESEARCH
- MOPED: Model Organism Protein Expression Database
- (2011) Eugene Kolker et al. NUCLEIC ACIDS RESEARCH
- PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
- (2011) P. V. Hornbeck et al. NUCLEIC ACIDS RESEARCH
- Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets
- (2011) Johannes Griss et al. PROTEOMICS
- Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
- (2011) Christopher R. Kinsinger et al. PROTEOMICS
- A posteriori quality control for the curation and reuse of public proteomics data
- (2011) Joseph M. Foster et al. PROTEOMICS
- Less label, more free: Approaches in label-free quantitative mass spectrometry
- (2011) Karlie A. Neilson et al. PROTEOMICS
- Peptide identification quality control
- (2011) Marc Vaudel et al. PROTEOMICS
- SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
- (2011) Marc Vaudel et al. PROTEOMICS
- Effective Representation and Storage of Mass Spectrometry-Based Proteomic Data Sets for the Scientific Community
- (2011) J. V. Olsen et al. Science Signaling
- Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research
- (2010) Juan Antonio Vizcaíno et al. Journal of Proteomics
- Peptide Identification from Mixture Tandem Mass Spectra
- (2010) Jian Wang et al. MOLECULAR & CELLULAR PROTEOMICS
- mzML—a Community Standard for Mass Spectrometry Data
- (2010) Lennart Martens et al. MOLECULAR & CELLULAR PROTEOMICS
- The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
- (2010) M. Gremse et al. NUCLEIC ACIDS RESEARCH
- The Ontology Lookup Service: bigger and better
- (2010) R. Cote et al. NUCLEIC ACIDS RESEARCH
- The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
- (2010) D. Szklarczyk et al. NUCLEIC ACIDS RESEARCH
- Iridovirus and Microsporidian Linked to Honey Bee Colony Decline
- (2010) Jerry J. Bromenshenk et al. PLoS One
- Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome
- (2010) Manuel Weiss et al. PROTEOMICS
- A guided tour of the Trans-Proteomic Pipeline
- (2010) Eric W. Deutsch et al. PROTEOMICS
- GeneCards Version 3: the human gene integrator
- (2010) M. Safran et al. Database-The Journal of Biological Databases and Curation
- Reanalysis ofTyrannosaurus rexMass Spectra
- (2009) Marshall Bern et al. JOURNAL OF PROTEOME RESEARCH
- False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule
- (2009) Nitin Gupta et al. JOURNAL OF PROTEOME RESEARCH
- Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry
- (2009) Lukas Reiter et al. MOLECULAR & CELLULAR PROTEOMICS
- NCBI Peptidome: a new public repository for mass spectrometry peptide identifications
- (2009) Douglas J Slotta et al. NATURE BIOTECHNOLOGY
- Credit where credit is overdue
- (2009) NATURE BIOTECHNOLOGY
- High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
- (2009) Paola Picotti et al. NATURE METHODS
- Universal sample preparation method for proteome analysis
- (2009) Jacek R Wiśniewski et al. NATURE METHODS
- Proteomics data repositories
- (2009) Michael Riffle et al. PROTEOMICS
- Recent developments in public proteomic MS repositories and pipelines
- (2009) Jennifer A. Mead et al. PROTEOMICS
- PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
- (2008) Eric W Deutsch et al. EMBO REPORTS
- Proteomics Based on Peptide Fractionation by SDS-Free PAGE
- (2008) Yassel Ramos et al. JOURNAL OF PROTEOME RESEARCH
- Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
- (2008) Sangtae Kim et al. JOURNAL OF PROTEOME RESEARCH
- Targeted Quantitative Analysis ofStreptococcus pyogenesVirulence Factors by Multiple Reaction Monitoring
- (2008) Vinzenz Lange et al. MOLECULAR & CELLULAR PROTEOMICS
- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
- (2008) Jürgen Cox et al. NATURE BIOTECHNOLOGY
- A database of mass spectrometric assays for the yeast proteome
- (2008) Paola Picotti et al. NATURE METHODS
- Human Proteinpedia: a unified discovery resource for proteomics research
- (2008) Kumaran Kandasamy et al. NUCLEIC ACIDS RESEARCH
- Human Protein Reference Database--2009 update
- (2008) T. S. Keshava Prasad et al. NUCLEIC ACIDS RESEARCH
- Discovery and revision of Arabidopsis genes by proteogenomics
- (2008) N. E. Castellana et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
- (2008) Michael Mueller et al. PROTEOMICS
- Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing
- (2007) Sebastian Klie et al. JOURNAL OF PROTEOME RESEARCH
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now