Table 1.

A partial list of commonly used database search software tools for proteomics analysis

Software name	Latest version	Source availability	Developer	URL and references
Proteome Discoverer	2.5	proprietary	Thermo Scientific	https://www.thermofisher.com/order/catalog/product/OPTON-30810
ProteinPilot	5.0.2	proprietary	Sciex	https://sciex.com/products/software/proteinpilot-software
ProteinLynx Global Server	3.0.3	proprietary	Waters	https://www.waters.com/waters/en_US/ProteinLynx-Global-SERVER-(PLGS)/nav.htm?cid=513821&locale=en_US
PaSER	2022	proprietary	Bruker	https://www.bruker.com/en/products-and-solutions/mass-spectrometry/ms-software/paser
MassHunter	11.0	proprietary	Agilent	https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis
MASCOT	2.8	proprietary	Matrix Science Inc	https://www.matrixscience.com/server.html; (Perkins et al. 1999)
MaxQuant	2.0.3.0	Freeware	Max Planck Institute of Biochemistry	https://www.maxquant.org/; (Cox and Mann 2008)
Byonic	4.2	proprietary	Protein Metrics Inc	https://proteinmetrics.com/byos/; (Bern et al. 2007)
Scaffold	5.1.0	proprietary	Proteome Software, Inc.	https://www.proteomesoftware.com/products/scaffold-5;(Searle 2010)
MSFragger	3.4	Freeware	University of Michigan	https://www.nesvilab.org/software.html;(Kong et al. 2017)
OMSSA	2.1.19	Freeware	The NIH intramural research program	https://ftp.ncbi.nlm.nih.gov/pub/lewisg/omssa/;(Geer et al. 2004)
Phenyx	Phenyx ®	proprietary	Geneva Bioinformatics (GeneBio)	https://ionsource.com/functional_reviews/Phenyx/phenyx-web.htm; (Colinge et al. 2003)
PRAKS DB	Xpro	proprietary	Bioinformatics Solutions Inc.	https://www.bioinfor.com/;(Zhang et al. 2012)
Protein Prospector	6.3.1	open source	University of California, San Francisco	https://prospector.ucsf.edu/prospector/mshome.htm;(Chalkley et al. 2005)
X!Tandem	2017.02.01	open source	University, Ghent, Belgium	http://www.thegpm.org/TANDEM/index.html;(Muth et al. 2010)