Software:Libra

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1 Getting the software
2 In a nutshell
3 More detail
4 Condition File Generator
5 Authors

Getting the software

This software is included in the current TPP distribution.

In a nutshell

Libra is a module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples.

More detail

More detailed information can be found at Sourceforge, including:

Command line syntax for using Libra
The condition file
Details about what Libra does
How accurate is the quantitation?

Condition File Generator

The Libra condition file generator is a useful web application.

For the 8-plex reagent, use the following condition file until more information is available about the contributions/corrections between the reporter ion peaks:

<?xml version="1.0" encoding="UTF-8"?>
<SUMmOnCondition>
  <fragmentMasses>
    <reagent mz="113.1" />
    <reagent mz="114.1" />
    <reagent mz="115.1" />
    <reagent mz="116.1" />
    <reagent mz="117.1" />
    <reagent mz="118.1" />
    <reagent mz="119.1" />
    <reagent mz="121.1" />
  </fragmentMasses>
  <isotopicContributions>
    <contributingMz value="1">
      <affected mz="2" correction="0.0" />
    </contributingMz>
    <contributingMz value="2">
      <affected mz="1" correction="0.0" />
      <affected mz="3" correction="0.0" />
    </contributingMz>
    <contributingMz value="3">
      <affected mz="2" correction="0.0" />
      <affected mz="4" correction="0.0" />
    </contributingMz>
    <contributingMz value="4">
      <affected mz="3" correction="0.0" />
    </contributingMz>
    <contributingMz value="5">
      <affected mz="3" correction="0.0" />
    </contributingMz>
    <contributingMz value="6">
      <affected mz="3" correction="0.0" />
    </contributingMz>
    <contributingMz value="7">
      <affected mz="3" correction="0.0" />
    </contributingMz>
    <contributingMz value="8">
      <affected mz="3" correction="0.0" />
    </contributingMz>
  </isotopicContributions>
  <massTolerance value="0.2" />
  <centroiding type="2" iterations="1" />
  <normalization type="1" />
  <targetMs level="2" />
  <output type="1" />
  <quantitationFile name="quantitation.tsv" />
  <minimumThreshhold value="20" />
</SUMmOnCondition>