Useful links

Tools

Scaffold Software Suite by Proteome Software: A suite of tools for visualising and validating complex MS/MS experiments. Scaffold is fully compatible with Mascot Server and Mascot Distiller.
GPMAW: Peter Højrup’s useful ready reckoner for molecular weights: General Protein / Mass Analysis for Windows
MS BLAST Search at Harvard: BLAST for sequences interpreted from mass spectra
mMass – Open Source Mass Spectrometry Tool: Various calculators for mass spectrometry and proteomics
Bachem peptide calculator: Free to use online tool for calculating physico-chemical properties of peptides from sequence

NCBI Taxonomy Homepage: How many legs does it have?
PaxDb: Protein Abundance Across Organisms: Whole genome protein abundance information
NAR Database of Databases: To accompany Nucleic Acids Research annual database issue
Max-Planck Unified (MAPU) proteome database: MAPU datasets can serve as reference proteomes in biomarker discovery
Genome Web: Proteomics and bioinformatics news.
SharedProteomics: Online proteomics community for sharing protocols, papers, news, questions, and more.
ABRF Discussion Forum: A good place for questions relating to proteomics and mass spectrometry
HUPO Proteomics Standards Inititative: Standards for data representation
Nature Methods: Nature Methods proteomics archive
neXtProt: neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.
jPOST: jPOST (Japan ProteOme STandard Repository/Database) integrates proteome datasets generated from multiple projects and institutions.
iProX: iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics.

PRIDE: The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files).
ProteomicsDB: ProteomicsDB is a joint effort of the Technische Universität München (TUM) and SAP AG. It is dedicated to expedite the identification of the human proteome
ProteomeXchange: The ProteomeXchange consortium has been set up to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories.
Chorus: Web-based storing, sharing, visualizing, and analyzing spectrometry files.
PeptideAtlas: The long term goal of the PeptideAtlas project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins