I plan to combine DDA and DIA for some future experiments (e.g., DDA for pooled QCs, DIA/SWATH for samples) and I was thinking about a workflow similar to R-based DaDIA approach (10.1021/acs.analchem.0c05022). I really like the software, so I wanted to ask if it's possible to align DDA and DIA data in MS-DIAL? As far as I understand it, it's only possible to decide batchwise if data is processed as DDA or DIA and it's not possible to align both data types in a straightforward manner. Do you plan to implement the possibility to analyze mixed batches of DDA and DIA data in future releases, e.g., by selecting datatype for each file in the sample list and align DDA and DIA files in the end?
Thanks a lot for your great work and best regards, Max
I was working with Waters travelling wave ion mobility data recently and was happy to realize that MS-DIAL treats TWIMS data. However, I am curious if you could integrate an alternative option for the TWCCSN2 calibration?
Instead of using coefficients A, exponent B and t0 an alternative method is typically used using a m/z dependent correction factor to determine the "corrected arrival times" tc from arrival times ta by taking into account the "EDC (Enhanced Duty Cycle) delay coefficient" C, which is an instrument dependent parameter (you find it in the .raw data folder in the methods). I think this is the approach typically used in Waters DriftScope and would be a nice as an option and often you use DriftScope to overwrite the initial mobcal.csv file with the new calibration function.
Until now I re-calculated CCS from arrival times using this approach which is not too time consuming, but automation would be nice and not all users will be aware on these differences.
I am using MS-DIAL 4.70 for LC-IM-QTOF data (Agilent and Waters, both operating in DIA mode) in a metabolomics/small molecules context. So far, I used CCS information "offline" for checking annotations using e.g. references from the CCS Compendium or in-house databases. This was working fine for me, but I recently tried using the CCS text libraries distributed via your website. MS-DIAL starts the process, but instead of running an analyis and showing the results, the process is interupted after a few seconds and I end up in the method window again (but without an error-message).
The text library was downloaded from the MS-DIAL website and was not changed. Additionally, I tried different combinations of ticking "use CCS for scoring", "use CCS for filtering" and nothing in the IM-settings window, but this didn't change the observation.
Is this a known issue and if yes: how can I work around it?
I really appreciate your work and think that the CCS library option would be a great additional feature!
Additionally, it would be great to have the option to set tolerances for CCS in % rather than absolute values. At least in the IM-MS context, tolerances are usually set in relative terms and tolerances can differ between different instrument classes (e.g. <+-1% for DT or <+- 2% for TW instruments).
