Software:Libra
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| Revision as of 18:05, 28 June 2007 Jeng (Talk | contribs) (→Condition File Generator) ← Previous diff |
Current revision Luis (Talk | contribs) (→More detail) |
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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 | ||
| Line 13: | Line 13: | ||
| * 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 |
[edit]
Getting the software
This software is included in the current TPP distribution.
[edit]
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.
[edit]
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?
[edit]
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.
[edit]
Authors
- Patrick Pedrioli: original code author of Quantitation
- Andrew Keller: peptide assignment to proteins within pipeline
- Nichole King: code maintenance/additions/corrections
