PythoMS: A Python Framework to Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data

Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear and visually compelling. The PythoMS framework introduces a library of classes and a variety of scripts that quickly perform time-consuming tasks: making proprietary output readable; binning intensity vs time data to simulate longer scan times (and hence reduce noise); calculate theoretical isotope patterns and overlay them in histogram form on experimental data (an approach that works even for overlapping signals); render videos that enable zooming into the baseline of intensity vs. time plots (useful to make sense of data collected over a large dynamic range) or that depict the evolution of different species in a time-lapse format; calculate aggregates; and provide a quick first-pass at identifying fragments in MS/MS spectra. PythoMS is a living project that will continue to evolve as additional scripts are developed and deployed.