Waters HDMSE Raw Data Visualization

Waters HDMSE Raw Data Visualization brad williams  2020-04-13

I have been testing the latest Skyline builds (20.1) and Skyline Daily ( and they both do not allow the raw data to be visualized for MS1 precursors. The raw data plot shows up blank and the MS/MS information is there. Has this been reported before? I have attached a screen capture to show an example. The datafile type is HDMSE.

Nick Shulman responded:  2020-04-13
Can you send us your Skyline document and one of your Waters .raw files?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

You should also send us your Waters raw data. I believe that means that you should zip up one of your .raw directories and send that to us.

You can upload those .zip files here:

When Skyline extracts chromatograms, Skyline remembers the "spectrum identifier" of each spectrum. Skyline represents these spectrum identifiers as a short list of numbers separated by dots. If Skyline is unable to show you some spectra, it might mean that the spectrum identifier that Skyline saved with the chromatogram is incorrect, or for some other reason, cannot be used to find the spectrum that Skyline is trying to show you.

We will be able to figure out what is going wrong when we see your files.
-- Nick
brad williams responded:  2020-04-16
Hi Nick,

Thank you for the reply. I uploaded the archived skyline file and an example raw data file. The file was compressed with WinRar and will need to be uncompressed back to the .raw form. I have uploaded a screen capture of the file names that have been uploaded to the Skyline datashare.

Thank you,