Table 1 A partial list of commonly used database search software tools for proteomics analysis
From: Recent advances in proteomics and metabolomics in plants
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 | |
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) |