- 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.
Training scoring parameters (ScoringParamGen)
The Generating Function of CID, ETD and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search
Sangtae Kim, Nikolai Mischerikow, Nuno Bandeira, J. Daniel Navarro, Louis Wich, Shabaz Mohammed, Albert J. R. Heck, Pavel A. Pevzner
Molecular & Cellular Proteomics, 9, 2840-2852, 2010.
A powerful tool for PTM discovery (Jan 2008, Journal of Proteome research, Vol 7. Issue 1)
From spectral networks to shotgun sequencing (June 2007, Nature Methods, Vol. 4 No. 6)
Identifying peptides without a database (May 2007, Journal of Proteome Research)
UCSD Computer Scientist Wins Young Investigator Award, Research on Snake Venom Proteins Highlighted (Nov 2006, UCSD)