Using mProphet at ISB
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| Put transition file into same directory as your data (mzML or mzXML format). | Put transition file into same directory as your data (mzML or mzXML format). | ||
| - | Go to that directory. | + | Log onto regis and go to that directory. |
| - | Then, on regis: | + | Then: |
| - | '''/proteomics/sw/mquest/bin/mInteract.pl -force -mmap -mmap_machine QTRAP -cycle 2.0 -mquest ./ -workflow LABEL_FREE''' | + | ==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. | -cycle is cycle time; used for QTRAP mzXML files only. | ||
| Line 28: | Line 30: | ||
| -force processes all files, even those that have already been processed. | -force processes all files, even those that have already been processed. | ||
| - | Other options for mmap_machine: TSQ, QQQ. If your files are mzML it doesn't matter what you put here. | + | 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. | 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 | ||
| - | To run mProphet, you need to have measured decoy peptides. See mProphet documentation for further information on this topic. Add -mprophet to the command line to run mProphet. | + | ==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. | ||
Revision as of 01:23, 26 August 2011
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.
