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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Suffix instead of Prefix pattern for decoys #66

Closed tivdnbos closed 5 years ago

tivdnbos commented 5 years ago

Hi all,

I was wondering if there's a possibility to use suffix patterns instead of prefix patterns with MS-GF+? And, if not, if there's a way to implement this in the code?

Best wishes,

sangtaekim commented 5 years ago

It's conceptually not difficult but will require code changes. I believe we don't have a plan to change it unless there's a strong need. If you're interested in changing it yourself, https://github.com/MSGFPlus/msgfplus/blob/master/src/main/java/edu/ucsd/msjava/msdbsearch/SuffixArrayForMSGFDB.java will be a good start.

FarmGeek4Life commented 5 years ago

Another option to effectively change the prefix to a suffix is by using a regular expression search and replace tool on the mzid.

One example that will work on a linux command line: sed -i 's/\(accession="\)XXX_\([^"]\+\)/\1\2_REVERSED/g' test.mzid XXX_ and _REVERSED can be changed to whatever they need to be.

tivdnbos commented 5 years ago

Thanks! I was able to fix it.

Best wishes, Tim