pLink2 freezes at "Complete first search"

[audrizzle]

I'm running a search that I've run before. It was successful in the past, but each time I try to run pLink2 for this particular file, it freezes at "Complete first search." and the "Save" and "Stop" button in the GUI are still grayed out, but the stop button is available. If I stop it and restart, it restarts from the beginning and stops at "Complete first search" again.

Here's the last few lines of my output file:
[pLink] Loaded 5000 spectra, 32930000 / 32950275
[pLink] Loaded 5000 spectra, 32935000 / 32950275
[pLink] Loaded 5000 spectra, 32940000 / 32950275
[pLink] Loaded 5000 spectra, 32945000 / 32950275
[pLink] Loaded 5000 spectra, 32950000 / 32950275
[pLink] Loaded 275 spectra, 32950275 / 32950275
[pLink] Complete First search.

Thanks in advance for any help!

[NorthblueM]

Given the large number of spectra extracted, it's likely that your data came from a Bruker timsTOF instrument. And if you used MSConvert to extract the MGF files, you probably forgot to check the "Combine ion mobility scans" option. Please remember to check it. In addition, since some spectra are lacking important information like the precursor ion charge, pLink crashes when trying to identify them.

When pLink loads MGF files, it requires complete spectrum information. You can filter out spectra with missing data to create new MGF files and then run pLink again. To remove problematic spectra from the MGF files, you can utilize the following python script tool: https://github.com/NorthblueM/pFindStudio-ToolScripts/tree/main/pLink_mgf_remove_illegal_spec .