Open Source System for Analyzing, Validating, and Storing Protein Identification Data

Abstract

This FAIRsharing record describes: The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.

Keywords

ServerComputer scienceIdentification (biology)DatabaseDatabase serverOpen sourceRelational databaseInterface (matter)ProteomeWorld Wide WebOperating systemBioinformaticsSoftware

Affiliated Institutions

Research Manitoba CA

Related Publications

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Pérez‐Riverol , Attila Csordás , Jingwen Bai +20 more

This FAIRsharing record describes: The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrome...

2018 Nucleic Acids Research 7132 citations

The Pfam protein families database in 2019

Sara El-Gebali , Jaina Mistry , Alex Bateman +13 more

This FAIRsharing record describes: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)....

2018 Nucleic Acids Research 4869 citations

ColabFold: making protein folding accessible to all

Milot Mirdita , Konstantin Schütze , Yoshitaka Moriwaki +3 more

Abstract ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold’s...

2022 Nature Methods 8663 citations

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Tony E. Lewis , Ian Sillitoe , Antonina Andreeva +21 more

This FAIRsharing record describes: Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The da...

2012 Nucleic Acids Research 57 citations

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere , Liis Kolberg , Ivan Kuzmin +4 more

Abstract Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched ...

2019 Nucleic Acids Research 5069 citations

Publication Info

Year: 2004
Type: article
Volume: 3
Issue: 6
Pages: 1234-1242
Citations: 688
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

Open Source System for Analyzing, Validating, and Storing Protein Identification Data

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

688

OpenAlex

Cite This

APA Style

                            
                                    Robertson Craig, 
                                
                                    John P. Cortens, 
                                
                                    Ronald C. Beavis
                                
                            (2004). 
                            Open Source System for Analyzing, Validating, and Storing Protein Identification Data. 
                            Journal of Proteome Research
                            , 3
                            (6)
                            , 1234-1242.
                            https://doi.org/10.1021/pr049882h

Identifiers

DOI: 10.1021/pr049882h