Hello, Within Libra and its condition file, the channel values (e.g. contributingMz and (affected) mz) refer to the ones that you have selected -- whether you select 2, 3, or all 8, in any arbitrary combination.
The correction values affect only isotopes that are plus/minus 1 or 2 Daltons from the channel in question (provided that there is an actual channel to measure at that m/z value). I'll illustrate how your values are used by answering your queries (*inline* below). On Thu, Aug 28, 2014 at 1:52 AM, Konstantinos Vougas <[email protected]> wrote: > Dear All, > > I have created a condition.xml file for the iTRAQ-8plex according to > Thermo's instructions (I am using an Orbitrap Elite) for the correction > values (see screenshot). > > I am also attaching the created condition.xml file. > > What I do not get and I need your help is the logic behind the "affected > mz" number. > For instance > > 1. > <contributingMz value="1"> > <affected mz="2" correction="0.018" /> > <affected mz="3" correction="0" /> > </contributingMz> > > This I suppose refers to 113. According to the screenshot I sent you the > 3rd column (% of +1) and not the second (% of -1) has the value of 1.8%. > Why is > > <affected mz="2" correction="0.018" /> > <affected mz="3" correction="0" /> > ?? > > *You are correct, this is the contribution from the 113 channel, or channel #1. From the values in your screenshot, 1.8% of this channel will fall +1 Daltons away, at 114, which is channel #2. This is what is encoded in the file.* > 2. > <contributingMz value="7"> > <affected mz="5" correction="0" /> > <affected mz="6" correction="0.0259" /> > <affected mz="8" correction="0" /> > </contributingMz> > > This I suppose refers to 119. Why is the correction of 2.59% applied to > affected mz="6" and what does 6 represent? Shouldn't it be 1-4 as the > columns? > > *Channel #7 is indeed 119. The -1 isotopic offset falls at 118, which is channel #6.* > and finally > > 3. > <contributingMz value="8"> > <affected mz="7" correction="0" /> > > This I suppose refers to 121. My correction of 3.58% for "% of -1" which > is the 2nd column is nowhere to be found. Instead I get an affected mz="7" > correction="0"!!! > > *For channel #8, the -1 isotopic correction falls at an m/z of 120. Since there is no channel at this m/z, no correction is encoded. The -2 isotopic offset falls at 119, which is channel #7, but the correction is set to zero -- this is what is in the file.* > > Can anybody explain this? > > > Hope this helps. --Luis -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
