Software:Libra

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==In a nutshell== ==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.+Libra is a module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples; it can also be used on TMT labeled samples. There is no limitation to the number of channels that Libra can quantitate against.
==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 by [http://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html downloading this file], including:
* Command line syntax for using Libra * Command line syntax for using Libra
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* How accurate is the quantitation? * How accurate is the quantitation?
-==Condition File Generator==+==Generating a Condition File==
-The [http://db.systemsbiology.net/webapps/conditionFileApp 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:+You can generate a condition file using the built-in utility within the TPP web UI (Petunia), or by using a text editor.
- +
- <?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== ==Authors==

Current revision

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 isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples; it can also be used on TMT labeled samples. There is no limitation to the number of channels that Libra can quantitate against.

More detail

More detailed information can be found by downloading this file, including:

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

Generating a Condition File

You can generate a condition file using the built-in utility within the TPP web UI (Petunia), or by using a text editor.

Authors

  • Patrick Pedrioli: original code author of Quantitation
  • Andrew Keller: peptide assignment to proteins within pipeline
  • Nichole King: code maintenance/additions/corrections
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