error message "The MasterScan does not exist"

[Andie]

Dear All,

I am new to lipidomics and been struggling to find a way to analyse some direct infusion data from bacteria lipids – someone from Thermo recommended LipidXplorer and is great!

I think I got my head around the concept as when I try the tutorials is all ok but when I did a test with one of my many samples, I get an error message.

I have extracted some bacterial membrane lipids and done MS and MS2 in negative and positive mode.

I have used an Exactive from Thermo.

One of my samples is Salmonella and I expect to have some PE’s, so I converted the thermo raw file into a mzML file. Loaded into import source tab and used the same settings as for the E.coli_neg tutorial example as I do not expect much difference. So, basically, the only difference is that I load my own file as the rest of the settings are the same as the tutorial. Yes, my resolution for MS1 was of 140,000 and for MS2 17,500 but I thought to make as little changes as possible now (later I know I need to change the settings as per my instrument and I will probably ask more questions again) to see if at least basics were correct.

I managed to convert the file successfully and I can see the MS1 and MS2 in the convertor so I am a bit lost. Any help is appreciated. The server does not accept my attachments so please see a few screenshots of my instrument settings, error message, the script from the tutorial I use and the converted file.

Any help is much appreciated!!