Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 66

Table 4.3
Peptide and protein identification software

Uninterpreted MS/MS database searching
ProbID ( 79 ) http://sashimi.sourceforge.net/software_mi.html

PepProbe http://bart.scripps.edu/public/search/pep_probe/

search.jsp

OMSSA ( 80 ) http://Pubchem.ncbi.nlm.nih.gov/omssa

Phenyx ( 81 ) http://www.genebio.com/products/phenyx /

Spectrum Mill http://www.home.agilent.com

X!Tandem ( 82 ) http://human.thegpm.org/tandem/thegpm_

tandem.html

MS-Tag ( 22 ) http://Prospector.ucsf.edu

Mascot
Server ( 19 )

http://www.matrixscience.com /

Protein
Pilot/Paragon
( 83 )

https://products.appliedbiosystems.com/ab/en/
US/adirect/ab?cmd = catNavigate2&catID =

601680&tab = DetailInfo

SEQUEST ( 8 ) http://www.thermo.com/com/cda/product/

detail/0„16483,00.html?CA = bioworks

XProteo http://xproteo.com:2698/

MyriMatch ( 84 ) http://www.mc.vanderbilt.edu/msrc/

bioinformatics/myrimatch/index.php

Sequence tag searching
GutenTag ( 85 ) http://fields.scripps.edu/GutenTag/

InsPecT ( 86 ) http://bix.ucsd.edu/

MultiIdent ( 87 ) http://www.expasy.org/tools/multiident /

Spider ( 88 ) http://proteome.sharcnet.ca:8080/spider.htm

MS-Seq ( 22 ) http://Prospector.ucsf.edu

Mascot
Server ( 19 )

http://www.matrixscience.com /

PepFrag ( 89 ) http://prowl.rockefeller.edu/prowl/pepfrag.html
Accurate mass and time tags
VIPER ( 24 )

http://omics.pnl.gov/software/VIPER.php

msInspect/AMT
( 90 )

http://proteomics.fhcrc.org/CPL/amt/

Spectral matching
P3 http://www.thegpm.org/PPP/index.html

SpectraST ( 91 ) http://www.peptideatlas.org/spectrast /

BiblioSpec ( 92 ) http://proteome.gs.washington.edu/software/

bibliospec/documentation/index.html

NoDup fields.scripps.edu/nodupe/index.html

MS-Clustering
( 93 )

http://bix.ucsd.edu/

(Continued)