Using mProphet at ISB
From SPCTools
mQuest and mProphet are a software suite for the analysis of SRM data. See [1] for literature reference, manual, and installation instructions.
To run mQuest, you need a tab-separated transition file with the following columns, only three of which are required:
- Q1 (required)
- Q3 (required)
- transition_group_id (required) -- a unique id for the transitions of one precursor
- stripped_sequence
- prec_z
- frg_type (y, b, etc.)
- frg_nr (3, 7, etc.) (The Excel formula MID() is useful for parsing y12 into y and 12)
- frg_z
- Isotype (heavy or light)
- protein_name
- CE
(See p. 6 of the manual for other columns you can provide.)
Put transition file into same directory as your data (mzML or mzXML format). Don't use symlinks.
Log onto regis and go to that directory. Then ...
mzXML Files
/proteomics/sw/mquest/bin/mInteract.pl -force -mmap -mmap_machine QTRAP -cycle 2.0 -mquest ./ -workflow LABEL_FREE
-cycle is cycle time; used for QTRAP mzXML files only.
-force processes all files, even those that have already been processed.
Other options for mmap_machine: TSQ, QQQ.
Other options for workflow: SPIKE_IN. Type /proteomics/sw/mquest/bin/mInteract.pl -help or -manual for more info.
mzML Files
mInteract doesn't yet work for mzML files, so you have to run mMap and mQuest separately.
/proteomics/sw/mquest/bin/mMap2.pl -force -machine=QTRAP -cycle=2.0 -strict ./ -mz "*.mzML" -trans transitions.tsv
-cycle is cycle time; used for QTRAP mzXML files only.
-force processes all files, even those that have already been processed.
-mzxml "*mzML" is a specification of the spectrum files to use; it is not needed if you have mzXML files and want to process all of them.
-machine -- for mzML it doesn't matter what you put here.
/proteomics/sw/mquest/bin/mQuest.pl -force -mrml "*_mrml.xml"
Sadly, you will have to specify the workflow interactively.
mProphet
To run mProphet, you need to have measured decoy peptides. See mProphet documentation for further information on this topic. Add -mprophet to the mInteract command line to run mProphet.
