Mass spectrometry

PRIDE - PRoteomics IDEntifications database
http://www.ebi.ac.uk/pride/

A standardized public database, which contains the proteomics (protein and peptide identification) and mass spectrometry data.

Tranche
https://www.proteomecommons.org/tranche/

It is a freely available file storage platform, which mainly stores the raw data.

URL not working as on 2 Feb 2015 (confirmed on 14 Nov 2016)

Peptide atlas
http://www.peptideatlas.org/

Annotates the genome information of different species using the protein and peptide information obtained from mass spectrometry data.

GPM - Global Protein Machine
http://gpmdb.thegpm.org/

Mainly stores the MS/MS data. It reprocess the data and stores the identified protein and peptide information in GPMDB.

Peptidome
http://www.ncbi.nlm.nih.gov/peptidome

NCBI Peptidome is a public repository that stores and freely distributes tandem mass spectrometry peptide and protein identification data. NCBI has discontinued the Peptidome repository but all the existing data and metadata files are indefinitely available at the FTP server ftp://ftp.ncbi.nih.gov/pub/peptidome/.

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Website states that the repository is discontinued and is in an offline mode; all the data files can be obtained from its FTP site (as on 14 Nov 2016)