Chromatogram information unavailable after importing mzML files

Chromatogram information unavailable after importing mzML files Andreas  2020-11-24

I am analyzing Lipid data in the Small Molecule Mode of Skyline. I can import the Sciex MRM wiff files. However, importing peak boundaries changed the first sample of the batch only. Therefore, I converted the wiff file to mzML files using Msconvert (ProteoWizard). Unfortunately, after importing the results as mzML some lipids could not be imported with certain samples (Chromatogram information unavailable, see attached files). Are there special parameter for Msconvert required for usage with Skyline?

Nick Shulman responded:  2020-11-24
If you have specified the "Explicit Retention Time" for your molecules in Skyline, you should make sure that that time is within the time over which the SRM chromatogram was collected. If the Explicit Retention Time is not within the time range of a chromatogram then Skyline will assume that the chromatogram was not intended for that molecule.

If you would like, you could send us your .wiff file (and the .wiff.scan that goes with it) and maybe the .mzML file too and we can figure out why the chromatograms are not showing up.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:
-- Nick
Andreas responded:  2020-11-24
Hi Nick

Is it possible to upload the data files at a less public place?

Cheers, Andreas
Nick Shulman responded:  2020-11-24
I will send you an email directly.