Computes interferences in SRM (Selected Reaction Monitoring) experiments.
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README.md

README.md

srmcollider

Computes interferences in SRM (Selected Reaction Monitoring) experiments.

Homepage

You can find our website (with an interactive tool) at SRMCollider.org.

Publication

This tool was published in April 2012 and can be cited as follows:

Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics. 2012 Aug;11(8):540-9. PMID 22535207Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics. 2012 Aug;11(8):540-9. PMID 22535207

Installation

For installation and further instructions, see here.

Running

There are several scripts in code/scripts/runscripts/ that will be installed and are useful for different types of analyses:

  • runcollider.py is the most generic way to run the SRMCollider for individual peptides and generate information about the uniqueness of their transitions.
  • run_uis.py is used for high-throughput analyses of a whole proteome and computes summary statistics on the number of unique ion signatures (UIS) for each peptide in the query set.
  • run_integrated.py is used for high-throughput analyses of a whole proteome and uses optimized code in C++ to speed up the analysis.
  • run_eUIS.py is used for computing extended UIS (eUIS) as described in Röst et al.

Webserver

The SRMCollider comes with a webserver which can be accessed online at SRMCollider.org. For more information on how to install the webserver locally, see here.

Development

See the README for developers.