How are XCMS's retention times calculated January 26, 2015, 05:38:49 PM 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 RTBlue: Peak centroid (of all points within rtmin:rtmax and mzmin:mzmax using rawEIC)Red: Peak maxoGreen: 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] Quote Selected Last Edit: January 26, 2015, 06:42:58 PM by nate
Re: How are XCMS's retention times calculated Reply #1 – January 26, 2015, 06:07:42 PM I have some updated information and refined questions.The reported RT of a peak is the RT of the scan which lies halfway between the peak bounds as determined by centWave (scmin/scmax). An interesting, related point is that peaks are always defined as an even number of scans wide. This also means that the resolution of retention time is at best the scan rate.I would like to do my own analysis of the peaks. But a stumbling point for me is the disparity between scmin/scmax (peak limits found by wavelets) and the rtmin/rtmax. Could someone help me understand how rtmin/rtmax are determined? Scmin/scmax also return -1 in some cases - which precludes my analysis using them.Why does this occur and do you have a suggestion for peak bounds to use in these cases? (rtmin/rtmax seem insufficient in cases as above, where the bounds are much larger than the peak)How are lmin/lmax involved?Thanks much,Nathaniel Quote Selected