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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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How can I use several spectrum files? #119

Open Wang-kaifei opened 3 years ago

Wang-kaifei commented 3 years ago

Hi,

I use a param file to send parameters. But when I fill in the absolute path of multiple spectrum files, the software can only search for the first file. So I want to ask if this feature is supported.

Best, --wangkaifei

Wang-kaifei commented 3 years ago

Hi,

I met this requirement by using the folder path, then generated multiple .mzid files, and used MzidToTsvConverter.exe to generate multiple .tsv files.

My question is when these files are calculated and filtered by Q-value, should they be combined or filtered separately for each file? Is there a way to merge and filter to produce one result file?

Looking forward to your reply!

Best, --wangkaifei

alchemistmatt commented 3 years ago

MS-GF+ operates on one spectrum file at a time. As you found, if you specify the input "file" as a directory path, all .mzML files in that directory are processed (I think that's true; this is from memory).

QValues are also calculated on a per-spectrum file basis. We do not have a tool to merge and filter multiple .tsv files. The closest thing I can think of is to combine them with the type command at the Windows command prompt:

type Results1.tsv > CombinedResults.tsv
type Results2.tsv >> CombinedResults.tsv
type Results2.tsv >> CombinedResults.tsv

The equivalent command on Linux is cat

cat Results*.tsv > CombinedResults.tsv
Wang-kaifei commented 3 years ago

Thanks a lot !