Table 10.25.2.

Commonly Used Search Algorithms for MS/MS Data Searching

Search algorithm	Availability	Compatible file formats	Vendor/source
Mascot	Commercial	pkm, mzData, mzXML, asc, pkl, dta, pks	http://www.matrixscience.com
OMSSA	Open source	dta, mzXML, mgf, pkl	http://pubchem.ncbi.nlm.nih.gov/omssa/
Peaks	Commercial	pkl, dta, mgf, anz, mzXML, mzData, RAW, wiff, baf, yep, d, dat	http://www.bioinformaticssolutions.com
Phenyx	Commercial	dta, pkl, mgf, bdtx, mzdata, mzXML	http://www.genebio.com
ProteinLynx	Commercial	mzXML, mzData, pkl, txt	http://www.waters.com
Paragon (in ProteinPilot)	Commercial	wiff, mgf, ABI	http://www.appliedbiosystems.com
Sequest (in BioWorks)	Commercial	RAW	http://www.thermo.com
SorcererSequest	Commercial	RAW, mzXML, dta, out, srf, pkl, mgf	http://www.sagenresearch.com
Spectrum Mill	Commercial	Agilent, RAW, wiff, pkl	http://www.chem.agilent.com
X!Tandem	Open source	dta, pkl, mgf	http://www.thegpm.org/TANDEM/