Issue with Peak Extraction

[ddlidded]

After the latest update, it seems that after clicking on a peak when the "Full" is filled in through the scan filter, it seems to decrease the ppm window to where the scans are not fully picked up. After adjusting the ppm window to a different value then back to the original, the problem goes away until you view the compound again through the bookmarks tab. Take a look at what I mean below:

After retyping the ppm window, the scans magically appear again, but not when accessing through bookmark tab!

It fixed the SIM scan issue, however this issue now occurs, if it could be addressed that would be fantastic! This is maven version 2.10.22. @PMSeitzer

[PMSeitzer]

Thanks for letting me know @ddlidded - I think what's going on is that the actual bookmarked peak itself is very narrow in RT (note the small circles), and the m/z range observed in that small set of scans is likely very small. The "missing" scans you are seeing are actually scans that are technically outside of the RT range of the peak.

I think the solution is to pick a wider peak - and there a few ways you can do that.

The easiest way to pick a larger pick is to define the peak manually using SHIFT + click and drag, over the RT range you want for the peak. That way you can either pick up or explicitly exclude long tails and shoulders, and deal with any other strange stuff.

Alternatively, you can modify the peak detection parameters, so that the peak RT bounds are automatically a little wider. You can increase the smoothing window, or adjust the RT bounds parameters (available in the options dialog).

[ddlidded]

@PMSeitzer Also, it seems that in negative mode, the scans are still not continuous when using polarity switching (even after extracting the negative mzXML file). See Image attached Below. Positive mode looks good, however negative mode does not. Please let me know if you need me to attach an example file for you.

Are both of these issues something that can be addressed in the next release? It is quite annoying to have to do that when clicking on a bookmark when this was never the case before. Not sure how hard it is to fix that, but would be appreciated!