Theropod: Software Tools to Analyze Externally Collected Selective Temporal Overview of Resonant Ions

Recent developments in charge detection mass spectrometry have allowed for the broad characterization of individual proteoforms and mixtures of proteoforms from individual ions collected in Orbitrap mass spectrometers. In this study, we describe Theropod, a set of software tools to perform Selective Temporal Overview of Resonant Ions (STORI) analysis from transients collected on an external digital oscilloscope. Using a relatively wide charge correction, we are able to calculate the uncharged mass of ubiquitin, myoglobin, carbonic anhydrase, enolase, and the Pierce Intact Protein Standard protein mixture. We can also identify post-translational modifications from the protein mixture and the individual protein samples. Theropod is available at https://github.com/clelandtp/Theropod.