SLoMo: Site Localisation of Modifications

SLoMo is a tool which enables researchers to localise sites of post-translational modifications to peptides identified in mass spectrometry experiments. For more information see

Bailey, CM; Sweet, SMM; Cunningham, DL; Zeller, MM; Heath, JK; Cooper, HJ; Journal of proteome research vol. 8, no. 4 (April 2009), p. 1965-1971
 
or take a look at the poster (435Kb) presented at the BSPR meeting, Cambridge 2008.

The current version has been tested with output from Sequest and OMSSA search engines.

Using SLoMo

SLoMo is a command line tool written in the Perl programming language. In order to run it, you will need a perl interpreter on your machine. If you're running Linux or OS X, then you'll most likely already have one. If you're running Windows, then we recommend you use Active State's ActivePerl package.

Click on the 'Download Now' button on their website to download the latest version.

Demo/Tutorial

Click Here to download a zip file containing some demo data for use with slomo along with a powerpoint file with instructions

Installing SLoMo

Slomo is available as a zip or tar.gz file. Simply click on the links below to download it, then unzip the files into a directory of your choice. To run make sure that all the prerequesites are install (see below) then type ./slomo --help (Linux etc), or perl slomo --help (windows) at the command prompt to see all the command line options you can use with SLoMo.

Installing pre-requesites

Once you've got a working perl installation, there are then some additional requirements in order to get slomo to run. All these packages are available from CPAN (Linux etc) or using the PPM tool (Windows ActivePerl). Slomo outputs HTML output files, to get some graphs in them as well you will also need gnuplot which are available from gnuplot website. Once you have installed gunplot on your system you will need to edit the slomo.ini file to tell slomo where gnuplot is for example:
[gnuplot]
  path = "/usr/bin/gnuplot" # for linux

--OR--

[gnuplot]
  path = "C:\Program Files\gnuplot\bin\wgnuplot.exe" # for windows

Windows Instructions

Start the perl package manager (PPM), which should be in Start Menu --> Programs --> ActivePerl 5.X.X build nnn Once the PPM has loaded you should get a window which looks something like this:

Using the search box find the following packages Mark each of these packages for install ...

And then click on the install button (green arrow pointing right) to install the packages.

Linux Instructions

Start a cpan session (perl -MCPAN -e shell) and do the following:
install DBI
install DBD-SQLite
install Algorithm::Combinatorics
install XML::SAX
During the install if you get the following:
------
Unsatisified dependencies detected diring [G/GR/GRANTM/XML-SAX-0.96.tar.gz]
XML::NamespaceSupport
Shall I follow them and prepend them to the que of modules we are processing right now? [yes]
------
Enter 'yes'

Finally if you want speedier XML parsing install Expat, install the expat libraries using either your favourite package manager, or download them from Expat's Sourceforge Page and then again from a cpan session do:

install XML::SAX::ExpatXS
When it asks:
-------
Do you want to alter ParserDetails.ini? [Y]
-------
Enter 'Y'