Useful links

Tools

NCBI Taxonomy Homepage
How many legs does it have?
GPMAW
Peter Højrup’s useful ready reckoner for molecular weights: General Protein / Mass Analysis for Windows
MS BLAST Search at EMBL
BLAST for sequences interpreted from mass spectra
mMass – Open Source Mass Spectrometry Tool
Various calculators for mass spectrometry and proteomics

Resources

PaxDb: Protein Abundance Across Organisms
Whole genome protein abundance information
Bioinformatics Links Directory
Comprehensive links directory from Ontario Institute for Cancer Research
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

Repositories

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

Fun

The Protein Colourer
And why not?