[Question] Centroiding of TimsTOF class objects about alphatims HOT 1 CLOSED

Dear @triston-groff . Thanks for the kind words, happy you like it!
The alphatims.bruker.centroid_spectra() option is used within the index_precursors function, which itself is used to aggregate multiple ddaPASEF scans and provide traditional MS2 spectra for (proteomic) identification (it is e.g. being called in the export_mgf function). I fully agree that those functions could benefit from severe refactoring and that they are not well documented or easily understood, for which I apologize.

The centroid_spectra function should probably be considered an internal function of alphatims and not be exposed like this throught the API, as it only has a single use case and indeed requires very specific arguments.

Alphatims purposefully does not do any data processing (with the exception of exporting mgf files and the required steps to do so) and is intended to handle the raw data directly. However, I recognize your need to centroid MS1 and MS2 data. For MS1 data, you should be able to use Bruker software (e.g. their feature finder). For MS2, this is more difficult as DDA and DIA provide different data and there is also the quadrupole to consider. That said, there might soon be some open-source Python packages released that should be able to do peakpicking/centroiding in diaPASEF data...;)

from alphatims.