In my LIBRA quantitation.tsv ouput, I see intensity values less than
the minimum threshold set in condition.xml (see below). Is my
condition file correct? When is this threshold applied?
Since cutoff didn't seem to have been applied, I'd like to ensure that
the condition file is configured properly in case this indicates other
undetected issues with my setup. Thanks
-Dave
Background info: Labeled 35ug peptides each with iTRAQ 8-plex reagents
(113, 114, 115, 116, 117, 118, 119). Acquired data using Agilent 6520
QTOF in centroid only mode. Ran through XTandem. Ran Libra using cmd
line, set Peptide prophet probability 0.85 (<0.05 error), used
condition.xml (see below).
<?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" />
</fragmentMasses>
<isotopicContributions>
<contributingMz value="1">
<affected mz="2" correction="0.0689" />
<affected mz="3" correction="0.0022" />
</contributingMz>
<contributingMz value="2">
<affected mz="1" correction="0.0094" />
<affected mz="3" correction="0.059" />
<affected mz="4" correction="0.0016" />
</contributingMz>
<contributingMz value="3">
<affected mz="1" correction="0" />
<affected mz="2" correction="0.0188" />
<affected mz="4" correction="0.049" />
<affected mz="5" correction="0.001" />
</contributingMz>
<contributingMz value="4">
<affected mz="2" correction="0" />
<affected mz="3" correction="0.0282" />
<affected mz="5" correction="0.039" />
<affected mz="6" correction="0.0007" />
</contributingMz>
<contributingMz value="5">
<affected mz="3" correction="0.0006" />
<affected mz="4" correction="0.0377" />
<affected mz="6" correction="0.0299" />
</contributingMz>
<contributingMz value="6">
<affected mz="4" correction="0.0009" />
<affected mz="5" correction="0.0471" />
<affected mz="7" correction="0.0188" />
</contributingMz>
<contributingMz value="7">
<affected mz="5" correction="0.0014" />
<affected mz="6" correction="0.0566" />
</contributingMz>
</isotopicContributions>
<massTolerance value="0.2" />
<centroiding type="0" iterations="1" />
<normalization type="1" />
<targetMs level="2" />
<output type="1" />
<quantitationFile name="quantitation.tsv" />
<minimumThreshhold value="15" />
</SUMmOnCondition>
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