Software:Libra

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 18:05, 28 June 2007
Jeng (Talk | contribs)
(→Condition File Generator)
← Previous diff		 Revision as of 18:38, 19 July 2007
Jtasman (Talk | contribs)
(updating link: cvs to svn)
Next diff →
Line 6: Line 6:
==More detail== ==More detail==
-More detailed information can be found at [http://sashimi.cvs.sourceforge.net/*checkout*/sashimi/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html Sourceforge], including:+More detailed information can be found at [http://sashimi.svn.sourceforge.net/viewvc/*checkout*/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html Sourceforge], including:
* Command line syntax for using Libra * Command line syntax for using Libra

Revision as of 18:38, 19 July 2007

Contents

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>

Authors

  • Patrick Pedrioli: original code author of Quantitation
  • Andrew Keller: peptide assignment to proteins within pipeline
  • Nichole King: code maintenance/additions/corrections
Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Software:Libra"
Personal tools