Mayu

From SPCTools

Mayu, developed by Lukas Reiter at ETH, calculates decoy-based false discovery rates (FDRs) for proteomics experiments. FDR is calculated at the level of peptide-spectrum match (PSM), peptide identification, and protein identification. Protein length and possibly other attributes are taken into account.

Mayu is not yet shipped with the TPP as of July 2009. It has to be installed separately. You can either download it from here: http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/ ... or you can run it on our regis cluster at ISB. My understanding is that everyone in Ruedi's group is entitled to an account on regis.

If you use regis, then Mayu is run automatically on iProphet results any time you use one of the scripts stored in /regis/sbeams/bin, such as /regis/sbeams/bin/tandem/runtandemsearch. Those scripts ultimately call another script, /regis/sbeams/bin/MayuPepXML.csh, to run Mayu. MayuPepXML.csh can be run on its own on either a PeptideProphet or an iProphet file. Mayu processes PSMs (peptide-spectrum matches) and thus it does not make sense to run Mayu on ProteinProphet output.

All of this assumes that you are familiar running the TPP from the unix/linux command line. Mayu is not yet accessible via Petunia.