Question

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

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9.3 years ago

InterestedScientist ▴ 30

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?

Proteomics • 2.6k views

ADD COMMENT • link updated 2.1 years ago by Ram 43k • written 9.3 years ago by InterestedScientist ▴ 30

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

ADD REPLY • link 9.3 years ago by Devon Ryan 104k

Ram · Accepted Answer · 2015-01-07

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9.3 years ago

Laurent ★ 1.7k

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

ADD COMMENT • link updated 4.5 years ago by Ram 43k • written 9.3 years ago by Laurent ★ 1.7k

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

ADD REPLY • link updated 4.5 years ago by Ram 43k • written 9.3 years ago by InterestedScientist ▴ 30

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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

ADD REPLY • link 9.3 years ago by Laurent ★ 1.7k