Software:Mayu

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This software is licensed under the [http://creativecommons.org/licenses/GPL/2.0/ 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. This software is licensed under the [http://creativecommons.org/licenses/GPL/2.0/ 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.
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<nowiki>*</nowiki> if this discriminant score is compatible with target decoy searching <nowiki>*</nowiki> if this discriminant score is compatible with target decoy searching

Revision as of 11:39, 29 October 2008

Mayu

Protein Identification False Discovery Rates

Mayu 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.


* 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

Mayu package v1.06

  • manual
  • software package
  • example data set
  • perl script to create target decoy databases


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
Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Software:Mayu"
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