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Method Article
Alexey I. Nesvizhskii
Nesvizhskii Lab / University of Michigan
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Database search has long been the preferred method for peptide identification in shotgun proteomics. While a wide range of database search tools exist and excel for conventional workflows, they are too slow for open database searching. To make open searching practical for routine analysis, we developed a novel database search tool called MSFragger that is over 100 times faster than most existing tools.
This protocol demonstrates how to perform database searching using MSFragger. Up-to-date downloads of MSFragger and associated documentation can be found at "nesvilab.org/software.html":http://nesvilab.org/software.html.
Keywords
Mass spectrometry, Proteome informatics, Proteomics, Software
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The authors declare no competing financial interests.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.pdf
MSFraggerParamGuide Guide to Search Parameters
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Posted 10 Apr, 2017
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Associated Publications
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
by Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, +2
Nature Methods (10 April, 2017)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Alexey I. Nesvizhskii
Nesvizhskii Lab / University of Michigan
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 10 Apr, 2017
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Database search has long been the preferred method for peptide identification in shotgun proteomics. While a wide range of database search tools exist and excel for conventional workflows, they are too slow for open database searching. To make open searching practical for routine analysis, we developed a novel database search tool called MSFragger that is over 100 times faster than most existing tools.
This protocol demonstrates how to perform database searching using MSFragger. Up-to-date downloads of MSFragger and associated documentation can be found at "nesvilab.org/software.html":http://nesvilab.org/software.html.
Figure 1
Figure 2
Figure 3
Figure 4
The authors declare no competing financial interests.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.pdf
MSFraggerParamGuide Guide to Search Parameters
Loading...
Associated Publications
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
by Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, +2
Nature Methods (10 April, 2017)