Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches

Peter B O’Connor,Yury O Tsybin,Joseph A Loo,Frederik Lermyte

doi:10.1007/s13361-019-02201-x

Abstract

In recent years, there has been increasing interest in top-down mass spectrometry (TDMS) approaches for protein analysis, driven both by technological advancements and efforts such as those by the multinational Consortium for Top-Down Proteomics (CTDP). Today, diverse sample preparation and ionization methods are employed to facilitate TDMS analysis of denatured and native proteins and their complexes. The goals of these studies vary, ranging from protein and proteoform identification, to determination of the binding site of a (non)covalently-bound ligand, and in some cases even with the aim to study the higher order structure of proteins and complexes. Currently, however, no widely accepted terminology exists to precisely and unambiguously distinguish between the different types of TDMS experiments that can be performed. Instead, ad hoc developed terminology is often used, which potentially complicates communication of top-down and allied methods and their results. In this communication, we consider the different types of top-down (or top-down-related) MS experiments that have been performed and reported, and define distinct categories based on the protocol used and type(s) of information that can be obtained. We also consider the different possible conventions for distinguishing between middle- and top-down MS, based on both sample preparation and precursor ion mass. We believe that the proposed framework presented here will prove helpful for researchers to communicate about TDMS and will be an important step toward harmonizing and standardizing this growing field.Graphical

Highlights

The past decade has witnessed tremendous progress in both top-down (TD) and native protein mass spectrometry (MS) [1]. This has been driven by technological evolutions, including improvements in ionization techniques, reduced-frequency multipoles for high-m/z transmission and isolation, and high-m/z detectors, e.g., time-of-flight and Correspondence to: Frederik Lermyte; e-mail: f.lermyte@warwick.ac.uk extended-mass-range ion cyclotron resonance (ICR) and Orbitrap Fourier transform mass spectrometry (FTMS) [2, 3]
The term Bnative electron capture dissociation^ was originally introduced in 2003 by Breuker and McLafferty to refer to a process presumably initiated by asymmetric charge partitioning during dissociation of the cytochrome c dimer within a heated transfer capillary and has recently been used by Kelleher and colleagues to describe essentially the same process occurring in the native ferritin complex [7,8,9]
The term Bnative ECD^ has been used by others to describe experiments in which a folded protein complex was irradiated with low-energy electrons within an ion cyclotron resonance (ICR) cell [10,11,12], a process that is obviously fundamentally different from that reported by Breuker and McLafferty

Summary

Introduction

The past decade has witnessed tremendous progress in both top-down (TD) and native protein mass spectrometry (MS) [1]. The most basic experiment, this entails the measurement of the mass of an intact protein or complex under denaturing or native solution conditions, respectively, without any controlled dissociation being performed.

Results

Conclusion