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Topic: Side/ Partial Peak artifacts (Read 32 times) previous topic - next topic

Side/ Partial Peak artifacts

Hi All,
I was wondering if there is an existing processing/ post-processing solution for side/ partial peak XCMS artifacts.

The first concerns m/z traces that are typically different by 0.01-0.1 Daltons from the main peak and usually within 0.2 minutes (~12s). Example: Images 1 & 2 below.

The second concerns m/z traces often of equivalent m/z but within 0.3 minutes/ 20s from a particularly wide peak. Increasing my upper limit peakwidth did not seem to fix the issue. Maybe bw is too small? Example: images 3 & 4.

From reading previous forums on related topics, increasing mzdiff to as much as 0.1 helps eliminate overlapping mass trace peaks (at the expense of overlapping and poorly resolved isomer peaks), but side peaks of the nature described above remained. Playing with the prefilter option does help eliminate a lot of these, but again some still remain. The instrument used is an Agilent Q-TOF so I'm not sure if the discussion on Orbitrap shoulder peaks applies (though one forum from many years back mentioned that Agilent peaks have problems with ringing).

Basic details:
R version 3.5.3
XCMS version 3.4.4

Code: [Select]
mset <- xcmsSet("NEG_10", 
                method = "centWave",
                peakwidth       = c(5, 40),
                ppm             = 30,
                noise           = 100,
                snthresh        = 8,
                mzdiff          = 0.05,
                prefilter       = c(5, 500),
                mzCenterFun     = "wMean",
                integrate       = 2,
                fitgauss        = TRUE,
                verbose.columns = FALSE

mset2 <- retcor(mset,
                method  = "obiwarp",
                profStep = 1,
                center = 5)

mset2 <- group(
  method  = "density",
  bw      = 3,
  mzwid   = 0.05,
  minfrac = 0.5,
  minsamp = 1,
  max     = 50)

mset3 <- fillPeaks(mset2)