Table III The availability of some software reviewed in the article
Database search
    MascotCommercial and free at http://www.matrixscience.com
    SEQUESTCommercial at http://thermo.com
    InSpecTOpen source at http://proteomics.ucsd.edu/Software/Inspect.html Free online at http://proteomics.ucsd.edu/LiveSearch/
    PEAKSCommercial at http://bioinfor.com Free online at http://bioinfor.com/peaksonline
    TandemFree at http://www.thegpm.org/TANDEM/
De novo sequencing
    PEAKSCommercial at http://bioinfor.com Free online at http://bioinfor.com/peaksonline
    PepNovoOpen source at http://proteomics.ucsd.edu/Software/PepNovo.html Free online at http://proteomics.ucsd.edu/LiveSearch/
    LutefiskOpen source at http://sourceforge.net/projects/lutefiskxp/
Tag homology search
    CIDentifyOpen source at http://faculty.virginia.edu/wrpearson/fasta/OLD/CIDentify/
    SPIDERFree online at http://bioinfor.com/spider
    OpenSeaBinary obtainable from Oregon Health & Science University
    MS-BLASTFree online http://dove.embl-heidelberg.de/Blast2/msblast.html
    FASTSFree online http://fasta.bioch.virginia.edu
    MS-HomologyFree online http://prospector2.ucsf.edu/prospector
    GutenTagAcademic free under license at http://fields.scripps.edu/downloads.php
Protein sequencing
    CHAMPSFree binary at http://monod.uwaterloo.ca/champs/software.html
    CSPSOpen source http://proteomics.ucsd.edu/Software/CompShortProtein.html