Software:Mayu
Mayu
Protein Identification False Discovery Rates
Mayu (Protein identification false discovery rates for very large proteomics datasets generated by tandem mass spectrometry) is a software package for the analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy.
Mayu is not a search engine and works with any* peptide-spectrum match discriminant score derived from a database search.
This software is licensed under the CC-GNU GPL version 2.0 or later. This software and associated documentation is provided "as is" and there is no warranty for this software.
Mayu is written in Perl. It was creatd by Lukas Reiter at the Swiss Federal Institute of Technology Zurich.
* if this discriminant score is compatible with target decoy searching
Software
For running Mayu install a perl interpreter and run the software from the unpacked zip file on a command line. See the manual for more details.
Download
- manual
- software package
- example data set
- perl script to create target decoy databases
Distribution with TPP
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.
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, in the following two examples:
MayuPepXML.csh interact-prob.pep.xml
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.
Features
- provides false discovery rates not only on peptide-spectrum match level (mFDR) but also on protein identification (protFDR) and peptide identification (pepFDR) level
- false discovery rates for single hits (single peptide-spectrum match protein identifications) and all but single hits (protein identifications with more than one peptide-spectrum match)
- analysis in dependence of the amount of data
- R plots
- provides tables for each input file that relate the discriminant score (e.g. PeptideProphet, xcorr, mascot ion score,...) to a peptide-spectrum match false discovery rate
Example Result Plots
perl Mayu.pl -B example.csv -C tardecdb.fa -H 41 -N 4 -O 15 -v -PmFDR -runR
- graphical characterization of the input search results: discriminant score vs. peptide-spectrum match false discovery rate ds_vs_mFDR.pdf
- a number of plots helping the user in selecting the appropriate filtering for the desired quality main.pdf