Can we see the file? And where is it from? It appears to be saying that there is no precursor m/z value, which is strange.

Thanks for using the Skyline support board,

Brian Pratt

If there isn't precursor information it might be a GC-MS NIST library collected using electron ionization. If that is the case, it won't be compatible with data collected using electrospray ionization and tandem mass spectrometry. Not sure if we support EI spectral libraries for use with GC-MS data in Skyline yet.

Mike

we've downloaded es-ms library from massbank.jp. Also tried https://github.com/MassBank/MassBank-data/releases/tag/2024.11. you can take it from here. in both cases there was a problem: skyline didnt like the "/" symbol in both precursormz and precursor type (pic1), so i changed it on ",". But after another problem occurred, and I even dont understand the source (pic2). Its said H2O is being substracted from the molecule with no O, and there are plenty of such problem. But in the library its ok (pic3). What should I do? there is no more even an option to skip such compounds with problems %(

Thanks, I will download that library and work with it. I am currently working on improving support for EI in Skyline, certainly a part of that is dealing with new dialects of MSP files. Though I still don’t know what water loss is supposed to mean with a molecule containing no oxygen? At any rate that should be handled more gracefully.

Skyline’s data model assumes that fragments have precursor ions, even if all that’s known is its mz, so precursor “N/A” just doesn’t work, but all the EI msp files I’ve been looking at do include precursor info so this isn’t normally a problem.

You can see the water loss error in the picture 2. checking the library, there is no such actions (pic3). The error with NA in precursorMZ you can see in the picture attached below.

best regards, Diana