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Table: a comparison of publicly (non-commercial) available mass spectrometry resources
Varsha Ravikumar (*Correspondence: Acharya KK, kshitish@ibab.ac.in)
 
Feature PRIDE Global Proteome Machine Peptide atlas Tranche Peptidome
Maintained By European Bioinformatics Institute (EBI-EMBL) The Global Proteome Machine Organization Institute for Systems Biology University of Michigan National Center for Biotechnology Information (NCBI)
Status Working Working Working Not Working Not Working
Raw data Not available Not available Available Available Available
Processed and identified spectral data Not available Available Available Not available Available
Annotations provided Detailed Very basic Basic Very basic Detailed
Identified spectral information Available Not available Not available Not available Not available
Prototypic peptide (peptide sequence found only in that specific protein) Not available Available Available Not available Not available
Data submission procedure First need to convert into PRIDE Xml format and then through FTP it is uploaded Uploaded through Web interface FTP Web interface Upload FTP
Spectral line alignment Not available Available Not available Not available Not available
Present statistics (till 3 April 2013) Identified proteins = 12,215,318, Identified peptides = 69,344,804, distinct peptides = 6,163,762, total experiments = 27,643 Identified Proteins = 87,506,014, Identified peptides= 710,337,996, distinct proteins =1704358, distinct peptides = 4220490 Identified Proteins (human) = 214576, Identified Proteins(mouse)= 136945, Distinct peptides (human)=455577, Distinct peptides (mouse)=377249 Not available Not available
Query methods Experiment accession number, Identification accession number, Peptide sequence, Reference (PubMed ID/Title/Author), IPI, Ensembl Id, Names (Species,Tissue, Disease ), BTO Experiment accession number, Identification accession number, Peptide sequence, Ensembl Id, BTO, Keywords Ensembl protein Id, IPI ID, Refseq protein identifier, Unigene identifier, gene name, uniprot identifier, Peptide accession, Peptide sequence Not available Not available
Information about post translational modifications (PTM) Available Available Not available Not available Available
Type of information present Peak list, Derived peptide and Protein IDs, Associated metadata Metadata, protein and peptide information, Gene ontology display, Amino acid analysis Peptide and protein information, Sample peptide map Raw data Raw data, Peptide identification information, Biological and methodological metadata
Information about the primary database PubMed Tranche, PubMed, Peptide atlas Human Protein Atlas, Global Proteome Machine, PubMed PubMed, Peptide atlas PubMed, GenBank, Gene
Conversion of protein id's (based on relevant dbs) Can't be done Can be done Can't be done Can't be done Can't be find
Tools/softwares used to handle data-sets Pride inspector (Visualization tool) Not available Not available Not available Not available
 
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