I am not sure I understand your question considering re-processing from identification in MS-DIAL.
For your first question: yes. For the second one: either you use another .msp file, either you change the identification parameters. And yes, it is redoing the alignment for all the peaks considering the parameters you changed could affect the alignment of other peaks.
You can chose another file format to load when clicking on the arrow on the right of "ABF file" (see screenshot attached). It is making things super easy, and no need to convert the data anymore.
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 did all my samples data processing following the exact parameters you gave me, but I still have problems with my IS: - One of my IS is still not found by MS-DIAL (one of those that were missing previously) - The other detected by MS-DIAL, which is better. But the identification using a .txt file as in-house library did not work, and the feature in the ion table present a high mass deviation compared to my IS mass (approx 13 ppm instead of < 5 ppm when I am checking with XCalibur).
One of the group I am processing a few samples were not spiked with the IS(3 vs 28 samples spiked). Do you think it can be related (even if it should not)?
Here is a link to download two of my .raw data and an excel file with the information you requested. I have the same problem in ESI negative, but with more IS not picked up by MS DIAL (7/24 not found), so I attached a .raw file in both modes: grosfi.ch/adm4hAq6bpD
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