extracting MS1 EIC from PRM data leads to huge slowdown or crash

[chubukov]

Mostly PRM data seems to works ok. We're able to extract parent/daughter m/z pairs, as well as EICs for MS1 masses.

However, if I try to extract the MS1 EIC for for the PRM parent m/z, I get some awful behaviour (with a large number of files loaded, it crashes, with a small number of files, it slows down a lot, and I get some very odd grass in the EIC plot). My suspicion is that what's happening is that the fragmentation events widget is trying to process every single scan and this ends up being a huge cpu/memory load

Sample files and source file uploaded to our egnyte folder in the 11_11_2020_prm_bug folder.

[saifulbkhan]

@chubukov I was unable to find a reliable way of automatically deducing MS/MS data-type encoded in samples. So in #1349, I have added an input prompt which appears after loading PRM or DDA sample types to confirm this from the user. If you select "PRM" there, you should not experience any issues that would have been happening due to the fragmentation spectra/events widget.

Once built, the Windows installer should be available here. Hopefully, your slowdown (and crashes) should go away.

[chubukov]

@saifulbkhan ok, thanks. I agree it might be tricky to decide exactly what kind of method you have only from the mzML (although possible, I think). But maybe instead of the dialog you could simply gate on the relevant parameter, which seems to be the number of scans in the function?

[saifulbkhan]

@chubukov Sorry, I did not understand. Do you mean the number of MS/MS scans? And in which function?

Implementation aside, did the separate PRM treatment help with your slowdown issues with large number of samples?