Hello, By "unable to get it to work using Libra", so you mean that you get bad results? Or does the software crash? I think that you are using the iTRAQ-8 reagent kit, which carry a mass of 304.205360 (see the Unimod entry for more detail); the mass you are using (144.1) applies to the 4-channel version of the reagent.
You can set the "normalization channel" in Libra as the channel that you want to use as a reference (i.e. assign abundance ratio of 1, adjust the other channels accordingly). Hope this helps, --Luis On Fri, Nov 9, 2012 at 6:18 AM, Armin <[email protected]> wrote: > 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. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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.
