Turbo SLoMo: high throughput protein modification localisation

Turbo SLoMo is a modified version of SLoMo a PTM site localisation tool created at Birmingham University. The original software can be found here: SLoMo

SLoMo is a software tool which can localise and score sites of protein modification in mass spectrometry data.

Turbo SLoMo has been created to allow high throughput modification site localisation using the SLoMo algorithm. Turbo SLoMo takes input from pepxml formatted mass spectrometry search results and MS/MS spectra in the MGF format. Modifications of interest can be specified via the command line along with batch options allowing large datasets to be broken down into smaller sets when using a computational cluster.

Proteomic Mass Spectrometry Group

[Genome Research Limited]

Installation

1. SLoMo and Turbo SLoMo are written in Perl which should already be installed on Linux/Unix/OSX systems. For Windows systems it is recommended you install ActivePerl
2. Once you have Perl installed on your system you will also need some additional packages to run the program, these can be installed from CPAN or ActivePerl's PPM tool. Please install the following packages:
   1. Algorithm-Combinatorics
   2. DBI
   3. DBD-SQLite
   4. XML-SAX
   5. XML-SAX-Expat
3. Turbo-SLoMo can then be downloaded here: Turbo-SLoMo FTP
4. Simply extract the archive and you are ready to go.

For help installing and using Turbo-SLoMo please contact James Wright.

Usage

1. Export Search Results

   SLoMo has been tested with Mascot, Sequest, and OMSSA. We use Turbo-SLoMo with mainly Mascot results.

   To extract Mascot 2.4 results in the correct format first go to the Mascot results page. On this page there is an export button, use this to export the results as first a pepxml file and then as an MGF file. If you have access to you Mascot server this process can be automated using the export_dat.pl found in the Mascot cgi folder. This export_dat.pl tool can also be used to convert Mascot Percolator datp files.

2. Run TurboSloMo:

   TurboSLoMo [options]

    

   --pepxml=<file name>

   Name of the pepXML file to load (ignored if --database specified)

   --output=<file name>

   Name of the output file to be created

   --omssafile=<file name>

   Name of the omssa tab file to load (ignored if --pepxml or --database specified)

   --database=<database>

   Use database <database> (created with --outdb option)

   --dbonly

   Create a database file only, do not score localisations

   --outdb=<database>

   Save the database generated from the input file to <database> (default: temp.db)

   --mgf=<file>

   Input MGF spectra file (default: input.mgf)

   --mod=<pattern>

   Analyse all modifications that match this pattern. E.g. -mod=phospho will process all phosphorylation modifications. Special case: "ALL" will analyse all mods if results file (default: ALL)

   --mode=<mode>

   Fragmentation mode e.g. cid or etd (use --validmodes to see list of all modes). Modes can be specified in the Slomo.ini file. (default:ecd)

   --help

   Print usage information

   --validmodes

   Print a list of valid strings to use with -mode extracted from Slomo.ini

   --batchn

   Number of jobs to split results into

   --batchid

   Job number to run (based on batchn number of jobs)

   --maxMod

   Maximum number of Mods in a single peptide for it to be processed. Large numbers of modifications in a single peptide can lead to massive computational overhead.

   --minMod

   Minimum number of Mods in a single peptide for it to be processed.

Publications

• A phosphoproteomic data analysis workflow for combinations of collision induced dissociation and electron transfer dissociation

  Mark O. Collins, James C. Wright, Matthew Jones, Julian C. Rayner and Jyoti S. Choudhary

  2013

• SLoMo: automated site localization of modifications from ETD/ECD mass spectra.

  Bailey CM, Sweet SM, Cunningham DL, Zeller M, Heath JK and Cooper HJ

  Journal of proteome research 2009;8;4;1965-71

  PUBMED: 19275241; DOI: 10.1021/pr800917p

Contact

For help installing and using Turbo-SLoMo please contact James Wright.