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European Bioinformatics Institute
http://www.ebi.ac.uk/
ExPASy Proteomics Server
http://www.expasy.org/
NCBI HomePage
http://www.ncbi.nlm.nih.gov/
Protein BLAST search protein
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on
Proteome Factory - Proteomics, Protein Analysis and Validation
http://www.proteomefactory.com/?gclid=CIjHwNPVk5ICFQ41egodRkcF7A
Proteomics Instruments
http://www.proteomicworld.org/InstrumentsPage.html?gclid=CO-M3PXUk5ICFRE3egodsWHx6w
UniProt
http://www.uniprot.org/
EMBL
http://www.embl.org/
GenBank
http://www.ncbi.nlm.nih.gov/Genbank/index.html
Mascot
http://www.matrixscience.com/search_form_select.html
Swiss-Prot
http://www.expasy.org/sprot/
Database of protein domains, families and functional sites
http://cn.expasy.org/prosite/
Lutefisk97: Rich Johnson's de novo sequence program
http://www.hairyfatguy.com/Lutefisk/
MassSearch:Computational Biochemistry Research Group
http://www.cbrg.ethz.ch/services/MassSearch
Mowse
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/emowse.html
MultiIdent, PeptIdent, and TagIdent: Swiss Institute of Bioinformatics, Geneva
http://www.expasy.ch/tools/
De novo sequence interpretation from UCSD
http://peptide.ucsd.edu/
PeptideSearch
http://www.narrador.embl-heidelberg.de/GroupPages/PageLink/peptidesearchpage.html
Protein Prospector
http://prospector2.ucsf.edu/prospector/mshome.htm
Prowl: Rockefeller University
http://prowl.rockefeller.edu/PROWL/prowl.html
Seattle Proteome Center proteomics tools
http://tools.proteomecenter.org/software.php
Sequest
http://fields.scripps.edu/sequest/index.html
On-line Sequence Analysis Tools
http://www.up.univ-mrs.fr/~wabim/english/logligne.html
CMS Molecular Biology Resource
http://mbcf.dfci.harvard.edu/cmsmbr/
Proteome Commons
http://www.proteomecommons.org/index.jsp
SPS Digest
http://www.swissproteomicsociety.org/digest/archives.html
Spectral Database for Organic Compounds,SDBS
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng
Systems Biology Database
http://www.proteinlounge.com/
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