Table 2.
Peptide spectrum matching pipelines supported by Skyline with BiblioSpec for spectral library-building.
| Peptide spectrum matching pipeline | Type | Creator | Peptide ID file | Spectrum file |
|---|---|---|---|---|
| Mascot | Proprietary | Matrix Science (Perkins et al 1999) | .dat | |
| ByOnic | Proprietary | Protein Metrics, Inc. (Bern, Cai, and Goldberg 2007) | .mzid | .MGF, .mzXML, .mzML |
| Comet/SEQUEST/Percolator | Open source | Dept Genome Sciences, University of Washington (Eng, Jahan, and Hoopmann 2013; Eng, McCormack, and Yates 1994; Kall et al 2007) | .perc.xml (.sqt) | .cms2, .ms2 |
| ID Picker (Myrimatch) | Open source | MSRC Bioinformatics, Vanderbilt University (Tabb, Fernando, and Chambers 2007) | .idpXML | .mzXML, .mzML |
| MaxQuant Andromeda | freeware | Max Planck Institute (Cox et al 2011) | msms.txt | |
| Morpheus | Open source | Coon lab, University of Wisconsin-Madison (Wenger and Coon 2013) | .pep.xml, .pep.XML, .pepXML | .mzXML, .mzML |
| MS-GF+ | freeware | Pevzner lab, UCSD (Kim et al 2010) | .mzid, .pepXML | .MGF, .mzXML, .mzML |
| OMSSA | Open source | NCBI (Geer et al 2004) | .pep.xml, .pep.XML, .pepXML | .mzXML, .mzML |
| PEAKS DB | Proprietary | Bioinformatics Solutions, Inc. (Zhang et al 2012) | .pep.xml, .pep.XML, .pepXML | .mzXML, .mzML |
| Proteomics Identifications (PRIDE) | EMBL-EBI (Martens et al 2005) | .pride.xml | ||
| Protein Pilot | Proprietary | SCIEX (Shilov et al 2007) | .group.xml | |
| Protein Prospector | Open source | UCSF Mass Spectrometry Facility (Baker and Clauser) | pepXML/mzXML | |
| Proteome Discoverer | Proprietary | Thermo | .msf | |
| Scaffold | Proprietary | Proteome Software (Searle 2010) | .mzid | .MGF, .mzXML, .mzML |
| Spectrum Mill | Proprietary | Agilent | .pep.xml, .pep.XML, .pepXML | .mzXML, .mzML |
| Trans-Proteomic Pipeline (TPP) | Open source | Aebersold lab, Institute for Systems Biology (Deutsch et al 2015) | pepXML/mzXML | |
| X! Tandem | Open source | Global Proteome Machine Organization (Craig and Beavis 2004) | .xtan.xml | |
| ProteinLynx Global SERVER (PLGS) - MSe | Proprietary | Waters | final_fragment.csv | |
| Custom | .ssl |