SRM Collider
version 1.4
Hannes Röst 2012

About

This page is about the SRM Collider. It will provide some information about the algorithm and a link to the source code.

The SRM Collider is intented as a tool to support experimental biologists in creating specific and, if possible, unique SRM-assays for a peptide in a given background. It will take your input transitions and compare them to all other transitions in a given background proteome and find interferences. It will report these interferences on a per-peptide basis, allowing a researcher to identify peptides that share many transitions with the target peptide.

Algorithm

The SRM Collider can analyse all transitions of a target peptide in a given background.

It will compare the transition of the query peptide to the complete list of transitions generated from the background genome. The program will consider 3 dimensions: Q1 mass, Q3 mass and retention time. If there is another transition from the background "close enough", it will report a so called "collision". The definition of "close enough" can be adjusted with the input form, by setting (like in a real experiment) Q1, Q3 and RT windows.

Retention times are not experimental but theortical and calulated using the "SSRCalc tool". Thus the reported values are not retention times but rather an hydrophobicity index that helps to estimate how close together two peptides elute. Please refer to the SSRCalc paper for more information.

It is also possible to calculate UIS (unique ion signatures) for peptides. This means that combinations of transitions are considered and analysed for uniqueness within a given RT window. In order to calculate global UIS, just set the RT window to a very large value. Please refer to the UIS paper for more information.

Download Data

The results of the analysis can be downloaded in CSV (comma separated values) format which is Excel and OpenOffice compatible. While the "collision analysis" can be performed in batches, UIS can only be calculated for one peptide at a time and only up to an order of 5. Otherwise, the resources of the webserver are used up.

Source Code

The source code can be obtained at Download.

Citation

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 22535207

CSS Bugs

Yes, we know that IE6 does not display our website well advise you to not use IE6. We also know that Firefox has a rendering bug under Linux which it does not have under Windows. We chose to make the Windows version look good.

Contact and Bug reports

Any questions? Contact me at roest <> at <> imsb.ethz.ch