Software:Mayu
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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 | ||
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| For running Mayu install a perl interpreter and run the software from the unpacked zip file on a command line. See the manual, pdf for more details. | For running Mayu install a perl interpreter and run the software from the unpacked zip file on a command line. See the manual, pdf for more details. | ||
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| <ul> | <ul> | ||
| - | <li>manual</li> | + | <li>manual</li> |
| - | <li>software package</li> | + | <li>software package</li> |
| - | <li>example data set</li> | + | <li>example data set</li> |
| - | <li>perl script to create target decoy databases</li> | + | <li>perl script to create target decoy databases</li> |
| - | </ul> | + | </ul> |
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| <ul> | <ul> | ||
| - | <li>provides false discovery rates not | + | <li>provides false discovery rates not |
| only on peptide-spectrum match level (mFDR) but also | only on peptide-spectrum match level (mFDR) but also | ||
| on protein identification (protFDR) and peptide | on protein identification (protFDR) and peptide | ||
| identification (pepFDR) level</li> | identification (pepFDR) level</li> | ||
| - | <li>false discovery rates for single hits (single | + | <li>false discovery rates for single hits (single |
| peptide-spectrum match protein identifications) and all but single hits | peptide-spectrum match protein identifications) and all but single hits | ||
| (protein identifications with more than one peptide-spectrum match)</li> | (protein identifications with more than one peptide-spectrum match)</li> | ||
| - | <li>analysis in dependence of the amount of data</li> | + | <li>analysis in dependence of the amount of data</li> |
| - | <li>R plots</li> | + | <li>R plots</li> |
| - | <li>provides tables for each input file that relate | + | <li>provides tables for each input file that relate |
| the discriminant score (e.g. PeptideProphet, xcorr, mascot ion | the discriminant score (e.g. PeptideProphet, xcorr, mascot ion | ||
| score,...) to a peptide-spectrum match false discovery rate</li> | score,...) to a peptide-spectrum match false discovery rate</li> | ||
| - | </ul> | + | </ul> |
| + | |||
| + | |||
| + | |||
| + | '''Example Result Plots''' | ||
| + | |||
| + | perl Mayu.pl -B example.csv -C tardecdb.fa -H 41 -N 4 -O 15 -v -PmFDR -runR | ||
| + | |||
| + | <ul> | ||
| + | <li>graphical characterization of the input search | ||
| + | results: discriminant score vs. peptide-spectrum match false discovery | ||
| + | rate ds_vs_mFDR.pdf</li> | ||
| + | <li>a number of plots helping the user in selecting | ||
| + | the appropriate filtering for the desired quality main.pdf</li> | ||
| + | </ul> | ||
Revision as of 15:23, 28 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, pdf for more details.
Download
- 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
