Assigning peaks and modeling ETD in top-down mass spectrometry

TL;DR

This paper introduces a workflow and Python software for assigning peaks and interpreting electron transfer reactions in top-down mass spectrometry, enhancing understanding of ion fragmentation and structural analysis.

Contribution

It provides a novel workflow and open-source software for analyzing electron transfer reactions in top-down mass spectrometry, aiding structural proteomics.

Findings

Effective peak assignment in electron transfer reactions

Improved interpretation of fragmentation patterns

Open-source Python tool available for researchers

Abstract

Among many techniques of modern mass spectrometry, the top down methods are becoming continuously more popular in the overall strive to describe the proteome. These techniques are based on fragmentation of ions inside mass spectrometers instead of being proteolytically digested. In some of these techniques, the fragmentation is induced by electron transfer. It can trigger several concurring reactions: electron transfer dissociation, electron transfer without dissociation, and proton transfer reaction. The evaluation of the extent of these reactions is important for the proper understanding of the functioning of the instrument and, what is even more important, to know if it can be used to reveal important structural information. We present a workflow for assigning peaks and interpreting the results of electron transfer driven reactions. We also present software written in Python and available under GNU v3 license.