I noticed that with the last version (4.80), when I do a partial reprocessing (I only tested reprocessing from identification, not from the alignment), it is redoing the processing from scratch. When selecting data processing/identification, we only have access to the tabs from identification, but once we are clicking "OK" to run, it starts from the peak detection step.
I guess it is a bug, but considering it is taking more time (+ memory, etc) while it was not necessary with the previous versions, it would be great if it could be fixed (except if there is a reason for this in the new version )
I have two internal standards missing in my data treatment results, despite several tries of data processing using recommended parameters and several tests using optimised parameters more in accordance with my LC MS method (we have an Orbitrap). They are not only not identified: the masses are not found.
The other IS (8/10) are found. I checked the raw data and the missing IS are detected with high intensities (>10E7) and have good peak shapes.
I thought it was a peak detection problem, so I tried: - several minimum peak height values (from 30,000 to 90,000) - different mass slice width (0.05 to 0.15) - the minimum peak width (5 to 15 scans) But it did not solved the problem.
I also did some test refining the data collection parameters, and alignment parameters, in combination with the peak detection parameters tested earlier, but nothing solved my problem.
Do you have any idea of what could be the problem? Thank you for your help.
(except if there is a reason for this in the new version