public MS/MS repositories :
- Pride: PRoteomics IDEntifications database
- Peptide Atlas: Annotation of genomes through expressed proteins
- GPMDB: Global Proteome Machine database
A raw data database for download:
- Tranche @ ProteomeCommons: A free and open source file sharing tool
Some identification databases:
- Human Proteinpedia: A community portal for sharing and integration of human protein data
- MAPU 2.0: Max-Planck Unified Proteome Database
- SwedCAD & SwedECD: Database of high resolution, high mass accuracy MS/MS Spectra derived from collision-associated dissociation (CAD) and electron capture dissociation (ECD).
- PepSeeker: A database of proteome peptide identifications for investigating fragmentation patterns
- YRC PDR: Yeast Resource Center Public Data Repository
Proteomics tools and MS/MS analysis pipeline:
- Promex: Protein Mass spectra EXtraction, A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS)
- OpenMS & TOPP: OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software. TOPP (The OpenMS Proteomics Pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem.
- GAPP: The Genome Annotating Proteomics Pipeline is a scalable grid-based pipeline for the automated analysis of proteomic MS data from disparate locations.
- Expasy proteomics tools: the Expasy server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.