Table 13.1.3.

Publicly and Privately Available Protein Identification and Quantitation Algorithms and Tools Used for Mass Spectrometry Data

Name	PMF	MS/MS ion-matching	Sequence tag	de novo	Quantitation	URL (or reference)
Mascot	x	x	x			http://www.matrixscience.com
ProbID		x				http://projects.systemsbiology.net/probid/
Protein Prospector	x	x	x			http://prospector.ucsf.edu
Sequest		x				http://fields.scripps.edu/sequest
Sonar		x				http://bioinformatics.genomicsolutions.com/index.html
X! Tandem		x				http://www.proteome.ca/opensource.html
Profound	x					http://prowl.rockefeller.edu/
GutenTag			x			http://fields.scripps.edu/GutenTag/index.html
ProSight PTMa			x			https://prosightptm.scs.uiuc.edu/
Lutefisk				x		http://www.hairyfatguy.com/lutefisk/
PEAKSb				x		http://www.bioinformaticssolutions.com/
SeqMS				x		http://www.protein.osaka-u.ac.jp/rcsfp/profiling/SeqMS.html
Sherenga				x		Dančık et al., 1999
ASAPRatio					x	http://tools.proteomecenter.org/windows.php
XPRESS					x	http://tools.proteomecenter.org/windows.php
Integrated platforms
BioAnalyst	x	x	x	x	x	http://www.appliedbiosystems.com
BioTools	x	x	x	x	x	http://www.bdal.com/biotools.html
BioWorks	x	x	x	x	x	http://www.thermo.com
Global Server	x	x	x	x	x	http://www.waters.com
RADARS	x	x				http://bioinformatics.genomicsolutions.com/index.html
SpectrumMill	x	x	x	x	x	http://www.chem.agilent.com

^aFrom intact proteins: “top-down” approach.

^bCombines de novo approaches against database searching.