Searching for a good search engine that is linux friendly and works with HCD data:

Question

[InterestedScientist]

Hi All,

I've tried a few different search engines but I thought I'd put this question out there so there can be an active discussion. Any opinions?

[Devon Ryan]

For those wondering (because they don't work on proteomics) what HCD is, see here for a start.

Answer 1

[Laurent]

I would suggest to get a go with MSGF+; it's cross-platform (java) and quite fast.

[InterestedScientist]

There doesn't appear to be a paper on MSGF+ out yet. Any idea when it's coming out?

[Laurent]

Indeed, the actual paper MSGF+ paper is not published yet (MS-GF+: Universal Database Search Tool for Mass Spectrometry, Sangtae Kim, Pavel A. Pevzner, submitted), but you can have a look at Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases, Sangtae Kim, Nitin Gupta and Pavel Pevzner, J. Proteome Res., 7 (8), 3354-3363, 2008. The actual software paper is not published yet, but the software has been around for quite a long time and has been widerly used.

Edit: By the way, both refs come from MSGF+'s README.txt file