Dear developers, users and especially Rune :-) Masswolf seems to have a problem with the low energy MSE data in MSE files. I should have 291 scans in both, the low and high energy scans (I checked this in Masslynx and also parsing the via Water's Databridge converted netCDF files). The high energy data has 291 scans, the low however changes to 365. If I look at the acquisitionNumbers then I can see that every other (5.) scan the low energy function "steels" a scan from the high energy function as you can clearly see here: low: 1 2 4 6 8 10 11 13 15 17 19 20 22 24 26 high: 3 5 7 9 12 14 16 18 21 23 25 27 You can also see that the file looks funny in the Insilicos viewer (random scan every other value) If I use waters Databridge to convert my MSE into two datafiles (netCDF), then convert them back into two waters .raw functions (high/ low energy file) and use masswolf to individually convert them into a mzXML function the scans are correct (both have 291 each) and look normal in the insilicos viewer. Centroiding does not have any influence on this. Does anyone have an idea what this could be caused? I verified this on different MSE files and all software is up2date.
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