MS-GFDB

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Contact: Sangtae Kim [sak008 (at) ucsd.edu]

Summary

• Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but the software tools to analyze tandem mass (MS/MS) spectra are lagging behind.


• While existing database search engines perform well on some types of spectra (e.g., Collision Induced Dissociation (CID) spectra of tryptic peptides), their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra, or spectra of non-tryptic digests.


• MS-GFDB is a MS/MS database search tool that is sensitive (it identifies more peptides than other database search engines) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).


• We also provide an user interface (ScoringParamGen) for training scoring parameters. Researchers using novel MS instruments or experimental protocols will benefit from this function. Training scoring parameters is as easy as running a database search.

Documentation (MS-GFDB)

Running MS-GFDB
Training scoring parameters (ScoringParamGen)