Fourier‐transform ion cyclotron resonance mass spectrometry for characterizing proteoforms

Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier‐transform ion cyclotron resonance mass spectrometry (FT‐ICR MS), with its ultrahigh mass‐resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top‐down, middle‐down, and native MS‐based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT‐ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in‐depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post‐translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT‐ICR MS and emerging applications, such as native top‐down FT‐ICR MS and high‐throughput top‐down FT‐ICR MS‐based proteomics at 21 T, are also covered. Historically, the information gleaned from FT‐ICR MS analyses have helped provide biological insights. We predict FT‐ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev