Skip to main content

Topics

This section allows you to view all Topics made by this member. Note that you can only see Topics made in areas you currently have access to.

Topics - nate

1
XCMS / How are XCMS's retention times calculated
Hi All,

I'm noticing some strange things regarding the reported RTs (xcmeSet@peaks[,"rt"]) from XCMS.  I'm using findPeaks.centWave.

My initial confusion was from the following data, a plot of the retention time difference between a M+0 peak and its isotope.  You can see the retention times come in discrete chunks rather than being continuously distributed.

[attachment=2:3bz8gt4p]discrete.png[/attachment:3bz8gt4p]

The bins appear to correspond to my scan rate which made me question how the RTs were being calculated - so I tried to figure out how this was done.  Unfortunately none of my methods reproduced the reported

[attachment=1:3bz8gt4p]a peak.png[/attachment:3bz8gt4p]
Black: xcms reported RT
Blue: Peak centroid (of all points within rtmin:rtmax and mzmin:mzmax using rawEIC)
Red: Peak maxo
Green: Half way through peak (rtmin:rtmax)


Additionally, I was surprised at how far off some the peaks were from my calculated centroid. For example this was good shaped peak where I can't figure out what the reported RT corresponds to.
[attachment=0:3bz8gt4p]rt_calc.png[/attachment:3bz8gt4p]

In summary:
1. How is the reported RT chosen - should it not be a continuous variable?
2. What do rtmin/rtmax correspond to (these are the limits of the above EICs)?

Thanks!
Ps.  I did not find the answer to these questions in the centWave paper.

[attachment deleted by admin]
2
CAMERA / Peak - adduct relationships
Hello all,

In working with CAMERA data I have been attempting to find hydrogen adducts and their corresponding sodium adducts.  I am wondering if this relationship is stored in the xsAnnotate object anywhere or if I should just repeat the search myself.

I currently find sodium adducts via rule_id as stored in an@derivativeIons.  I can then find hydrogen adducts within that psg in the same manner.  I am wondering if the information linking a specific M+H to its M+Na (or eg. M+Na to M+K) is stored anywhere?  I havent been able to find it - an@annoID$parentID isn't populated and no other an@derivativeIons fields seem applicable.

Thanks for the help,
Nate