Error in negative mode mzML file import

Error in negative mode mzML file import chang_he  2024-01-09 14:44

Hi, skyline support team,

I exported Waters Unifi analysis files to mzML and tried to import the data into Skyline 23.1. The following error was reported:

"At 2:42 PM:
Failed importing results file 'C:\Users\che\Desktop\Test\2_3_mix_6pt25uM [1A,5] [3].mzml'.
This document contains only negative ion mode transitions, and the imported file contains only positive ion mode data so nothing can be loaded."

It seemed like Skyline could not recognize the mzML file as negative mode. Is there a good way to fix this issue?

Thank you.

Brian Pratt responded:  2024-01-09 15:48

How did you do the conversion to mzML? And can you provide a copy of the file for us to look at?

Thanks for using the Skyline support board,

Brian Pratt

chang_he responded:  2024-01-09 17:08

Hi, Brian,

Thank you for the prompt response.

What I did previously was exporting the analysis results in Unifi to mzML files (other format options are mascot generic format, excel, labelled column spectra etc) . I think this process might have left out some information since I couldn't see any readable spectra in seeMS. I just converted the raw file to mzML with MSConvert and it worked!

Thank you.