Using mProphet at ISB
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| mQuest and mProphet are a software suite for the analysis of SRM data. See [http://www.mprophet.org] for literature reference, [http://www.mprophet.org/download/Manual.pdf manual], and installation instructions. | mQuest and mProphet are a software suite for the analysis of SRM data. See [http://www.mprophet.org] for literature reference, [http://www.mprophet.org/download/Manual.pdf manual], and installation instructions. | ||
| - | To run mQuest, you need a tab-separated transition file with the following columns, only three of which are required: | + | To run mQuest, you need a tab-separated transition file with the following columns, only three of which are required. Call this file transition_list.tsv: |
| *'''Q1 (required)''' | *'''Q1 (required)''' | ||
| *'''Q3 (required)''' | *'''Q3 (required)''' | ||
| Line 16: | Line 16: | ||
| (See p. 6 of [http://www.mprophet.org/download/Manual.pdf the manual] for other columns you can provide.) | (See p. 6 of [http://www.mprophet.org/download/Manual.pdf 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. | + | Put transition file into the same directory as your data (mzML or mzXML format). Don't use symlinks. |
| Log onto regis and go to that directory. Then ... | Log onto regis and go to that directory. Then ... | ||
| - | ==mzXML Files== | + | ==Set up environment variables== |
| - | '''/proteomics/sw/mquest/bin/mInteract.pl -force -mmap -mmap_machine QTRAP -cycle 2.0 -mquest ./ -workflow LABEL_FREE''' | + | As of March 2013, the most functional versions of the software are in some directories maintained by Terry Farrah. To use these versions, first define some environment variables: |
| - | -cycle is cycle time; used for QTRAP mzXML files only. | + | If you use the bash shell: |
| - | -force processes all files, even those that have already been processed. | + | '''MPRO_DIR_OLD=/proteomics/sw/mquest.x.x.x/bin/''' |
| - | Other options for mmap_machine: TSQ, QQQ. | + | '''MPRO_DIR_NEW=/proteomics/tfarrah/mprophet/11-15-11_download/mQuest_mProphet/mQuest/bin/''' |
| - | Other options for workflow: SPIKE_IN. Type /proteomics/sw/mquest/bin/mInteract.pl -help or -manual for more info. | + | (If you use C-shell or similar, precede each of these commands with the word <i>set</i>.) |
| - | ==mzML Files== | + | Set your machine type (TSQ, QTRAP, or QQQ): |
| - | 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''' | + | '''MACHINE=TSQ''' |
| - | -cycle is cycle time; used for QTRAP mzXML files only. | + | If your data is label-free: |
| - | -force processes all files, even those that have already been processed. | + | '''MPRO_DEF=label_free.def''' |
| - | -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. | + | If your data is spiked with heavy-labelled peptides: |
| - | -machine -- for mzML it doesn't matter what you put here. | + | '''MPRO_DEF=spike-in.def''' |
| + | |||
| + | Now, copy the appropriate params file to your directory: | ||
| + | |||
| + | '''cp /proteomics/sw/mquest.x.x.x/conf/$MPRO_DEF .''' | ||
| + | |||
| + | ==Run mMap== | ||
| + | |||
| + | '''$MPRO_DIR_OLD/mInteract_TF.pl -mMap -input ./ -trans transition_list.tsv -def $MPRO_DEF -mmap_machine $MACHINE -v -force -strict | ||
| + | |||
| + | ==Run mQuest== | ||
| + | |||
| + | '''$MPRO_DIR_OLD/mInteract_TF.pl -mQuest -input ./ -def $MPRO_DEF -v -force''' | ||
| + | |||
| + | -force processes all files, even those that have already been processed. | ||
| - | '''/proteomics/sw/mquest/bin/mQuest.pl -force -mrml "*_mrml.xml" ''' | + | ==Run 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. There are bugs and results are produced only for some datasets. | ||
| - | Sadly, you will have to specify the workflow interactively. | ||
| - | ==mProphet== | + | Type /proteomics/sw/mquest.2.0.3/mQuest/bin/mInteract.pl -help or -manual for more info. |
| - | 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 23:16, 1 March 2013
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. Call this file transition_list.tsv:
- 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 the same directory as your data (mzML or mzXML format). Don't use symlinks.
Log onto regis and go to that directory. Then ...
Contents |
Set up environment variables
As of March 2013, the most functional versions of the software are in some directories maintained by Terry Farrah. To use these versions, first define some environment variables:
If you use the bash shell:
MPRO_DIR_OLD=/proteomics/sw/mquest.x.x.x/bin/
MPRO_DIR_NEW=/proteomics/tfarrah/mprophet/11-15-11_download/mQuest_mProphet/mQuest/bin/
(If you use C-shell or similar, precede each of these commands with the word set.)
Set your machine type (TSQ, QTRAP, or QQQ):
MACHINE=TSQ
If your data is label-free:
MPRO_DEF=label_free.def
If your data is spiked with heavy-labelled peptides:
MPRO_DEF=spike-in.def
Now, copy the appropriate params file to your directory:
cp /proteomics/sw/mquest.x.x.x/conf/$MPRO_DEF .
Run mMap
$MPRO_DIR_OLD/mInteract_TF.pl -mMap -input ./ -trans transition_list.tsv -def $MPRO_DEF -mmap_machine $MACHINE -v -force -strict
Run mQuest
$MPRO_DIR_OLD/mInteract_TF.pl -mQuest -input ./ -def $MPRO_DEF -v -force
-force processes all files, even those that have already been processed.
Run 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. There are bugs and results are produced only for some datasets.
Type /proteomics/sw/mquest.2.0.3/mQuest/bin/mInteract.pl -help or -manual for more info.
