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.)
• 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).

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 -workflow LABEL_FREE ./

-workflow: see above

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.