obiwarp error: Found gaps: cut scantime-vector at ...
Dear obiwarp-experts,
I’d like to understand a problem better that occurs when I use obiwarp for retention time correction. I think it is a similar or the same problem as mentioned in these posts: http://http://metabolomics-forum.com/viewtopic.php?f=8&t=494 and http://http://metabolomics-forum.com/viewtopic.php?f=8&t=536:
“Found gaps: cut scantime-vector at XY.Z seconds”
The original raw-data is acquired on a Thermo-Q Exactive as MS1 with data-dependent MS2-spectra. The raw data were converted with ProteoWizard to mzXML, BUT only the MS1-level.
While trying to perform retention correction using obiwarp on those data files containing only MS1 spectra for some chromatograms I get the following error:
xs.grp.rt <- retcor.obiwarp(xs.grp, plottype = "deviation")
Processing: ABCD_pos Found gaps: cut scantime-vector at XY.Z seconds
On closer inspection of the flagged chromatogram at the mentioned time I can see an empty scan, the presumably problematic gap (see figures below). But the further I zoom in the more gaps I see which is not surprising due to the data-dependent MS2. For some reason (which I haven’t figured out yet) in some chromatograms one gap is larger than the others, which seem to be problematic for obiwarp.
What I would like to know is: Is there a maximum gap-size that obiwarp can handle and anything above provokes this error? Is it possible to correct this problem, so obiwarp can handle such chromatograms? And why doesn’t the rector.peakgroups-method produce the same error? Why can rector-peakgroups handle the scan-gap but rector.obiwarp cannot? :?:
Regards,
Jan
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