Depending on the type of MS data used in the experiment, the BioPharma Finder application uses one of the following to deconvolve MS spectra for top down analysis:

  • For full-scan MS data, the application uses a deconvolution algorithm (Xtract or ReSpect) to transform a charge state series into a molecular mass, similar to the process used for intact mass analysis.
  • To do this, the application identifies multiple peaks in the mass spectrum associated with different charge states of the same component and displays information about the mass and abundance of that component.
  • See "Deconvolution algorithms" in the Intact Mass Analysis User Guide.
  • For MS2 data, the application uses features of the ProSight Lite application to process the deconvolved MS2 data.
  • To do this, the application produces fragment maps with fragment mass labels for the found matched components (and their respective PTMs, if applicable).