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 written in Perl and accepts pepXML files, generated by either PeptideProphet or iProphet, as input.

Mayu is shipped with the TPP as of TPP v4.3.0, scheduled to be released in late July 2009. It can be found in trans_proteomic_pipeline/extern/Mayu. You can also download the Mayu software from here: http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/.

It can be handy to run Mayu using the ISB-written wrapper MayuPepXML.csh, found in the same directory. Whereas Mayu.pl must be invoked from the directory containing the script, MayuPepXML.csh allows you to run Mayu on any pepXML file from within any directory, as follows:

MayuPepXML.csh interact-prob.pep.xml

Or,

MayuPepXML.csh /regis/sbeams/archive/youngah/HsUrine/HsNormFemUrine_163A/SPC_HsNIST2.0/interact-ipro.pep.xml

Output will be copied into the same directory as the input pepXML file.

Of course, if the directory containing the script is not in your $PATH (enter "echo $PATH" to find out), you will have to enter the entire pathname of the script, as in this example (your pathname will be different):

/regis/sbeams/bin/Mayu/Mayu.pl interact-prob.pep.xml

MayuPepXML.csh uses a basic parameter set when calling Mayu. You can change the parameters by copying and editing the script.

Mayu is not yet available via Petunia. It must be run from the Unix/Linux command line.