IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry

Top-down proteomics has emerged as a transformative method for the analysis of protein sequence and post-translational modifications (PTMs). Top-down experiments have historically been performed primarily on ultrahigh resolution mass spectrometers due to the complexity of spectra resulting from fragmentation of intact proteins, but recent advances in coupling ion mobility separations to faster, lower resolution mass analyzers now offer a viable alternative. However, software capable of interpreting the highly complex two-dimensional spectra that result from coupling ion mobility separation to top-down experiments is currently lacking. In this manuscript we present a software suite consisting of two programs, IMTBX (“IM Toolbox”) and Grppr (“Grouper”), that enable fully automated processing of such data. We demonstrate the capabilities of this software suite by examining a series of intact proteins on a Waters Synapt G2 ion-mobility equipped mass spectrometer and compare the results to the manual and semiautomated data analysis procedures we have used previously.