Proteomics tools

Skyline – A open source software for analysis of PRM/DIA data

MaxQuant – A freely-available software for searching mass spec data.

Proteome Discoverer – A Thermo Scientific software with SEQUEST HT and Mascot search algorithms.  

Mascot – Online search for peptide mass fingerprint and protein ID.

Protein-protein interaction networks

String – A system-wide database for visualization of known and predicted protein-protein ienteractions .

BioGrid – A curated database of PTMs, protein, genetic and chemical interactions.

Repositories

ProteomicsDB – ProteomicsDB is a joint effort of the Technische Universität München (TUM) and SAP AG. It has a quantitative atlas of proteome, phosphoproteome, and transcriptome of 30 tissues of Arabidopsis.

ProteomeXchange – The ProteomeXchange consortium has been set up to provide a coordinated submission of MS proteomics data.