Software:Libra
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| ==Condition File Generator== | ==Condition File Generator== | ||
| The [http://db.systemsbiology.net/webapps/conditionFileApp Libra condition file generator] is a useful web application. | 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: | ||
| + | |||
| + | <?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== | ||
Revision as of 18:05, 28 June 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
