We maintain a list of freely available on-line proteomics databases, tools, and tutorials. Please let use know if you have any suggestions for this page.

Mass Spectrometry Databases and Depositories
Mass Spectrometry Database Search Engines
Protein Sequence and Domain Databases
Protein Sequence Searching
Sequence Alignment
Computational Resources

Mass Sectrometry Databases and Depositores

• Proteome Commonns - A list of proteomics data sets.
• OPD - Open Proteomics Database, OPD is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 1,200,000 spectra representing experiments from 4 different organisms.
• Proteomics World - ProteomicWorld provides a list of proteomics databases

Mass Sectrometry Database Search Engines

• X!Tandom - An open-source MS/MS search engine. It is very fast.
• Mascot - A popular commercial search engine for PMF and MS/MS. The link points to a free on-line version. KU researchers may access a full version in APL.
• ProteinProspector - a suite of proteomics tools developed at UCSF.

Protein Sequence and Domain Databases

• SWISS-PROT & TrEMBL
• PDB - protein 3D structure database
• InterPro - a useful resource for whole genome analysis and proteome analysis
• ExPASy - dedicated to the analysis of protein sequences and structures as well as 2-D PAGE

Sequence Searching

• BLAST @ NCBI
• FASTA @ EMBL-EBI
• Bioccelerator @ EMBL - Fast and Sensitive Smith-Waterman, Profile and Frame-shifting Database Searches.

Computational Resources

• CPAN - Comprehensive Perl Archive Network
• Bioperl - Open source Perl tools for bioinformatics, genomics and life science research.
• Biojava - Open-source project dedicated to providing Java tools for processing biological data
• Genamics SoftwareSeek - A respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.

Sequence Alignment

• USC Sequence Alignment Server - align 2 sequences with all possible varieties of dynamic programming
• T-COFFEE - multiple sequence alignment
• http://www.ebi.ac.uk/clustalw/ - multiple sequence alignment