Hi all
I’m performing the analysis of an iTRAQ data for the first time, I have
files in .mzML format. The petides were labelled with two iTRAQ reagents
117 and 119.
I am able to run the data through the pipeline (X!Tandem, peptide prophet ,
protein prophet ) without quantitation, however I am unable to get it to
work using Libra.
Firstly, I’ve added these lines to the “modifications” section of the
tandem parameters file:
<note type="input" label="residue, modification
mass">144.102063@[,144.102063@K</note>
<note type="input" label="residue, potential modification
mass">144.102063@Y</note>
Is this correct?
Secondly, for the Libra condition file I selected the commonly used values
for an iTRAQ 8-channel and deselected the labels that are not in my dataset?
this is the Libra condition file that I used:
<?xml version="1.0" encoding="UTF-8"?>
<SUMmOnCondition>
<fragmentMasses>
<reagent mz="117.1" />
<reagent mz="119.1" />
</fragmentMasses>
<isotopicContributions>
<contributingMz value="1">
<affected mz="2" correction="0" />
</contributingMz>
<contributingMz value="2">
<affected mz="1" correction="0.0014" />
</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>
Also, to what do I set the "Normalization channel"
Any help and advice would be appreciated
Thank you
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To view this discussion on the web visit
https://groups.google.com/d/msg/spctools-discuss/-/2kwPGA4LyVsJ.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
