Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Useful links


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.
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.
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


ProteomicsDB is a joint effort of the Technische Universit√§t M√ľnchen (TUM) and SAP AG. It is dedicated to expedite the identification of the human proteome
The ProteomeXchange consortium has been set up to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories.
Web-based storing, sharing, visualizing, and analyzing spectrometry files.
The long term goal of the PeptideAtlas project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins