Deconvolution in mass spectrometry based proteomics

Mass spectrometry (MS) has played a vital role across a broad range of fields and applications in proteomics. The development of high-resolution MS has significantly advanced biology in areas such as protein structure, function, post-translational modification and global protein dynamics. The two most widely used MS ionization techniques in proteomics are electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). ESI typically yields multiple charge values for each molecular mass and an isotopic cluster for each nominal mass-to-charge (m/z) value. Although MALDI mass spectra typically contain only singly charged ions, overlapping isotope patterns can be problematic for accurate mass measurement. To overcome these challenges of overlapping isotope patterns associated with complex samples in MS-based proteomics research, deconvolution strategies are being used. This manuscript describes a wide variety of deconvolution strategies, including de-isotoping and de-charging processes, deconvolution of co-eluting isomers or peptides with different sequences in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes, and data analysis in intact protein mass determination, ion mobility MS, native MS, and hydrogen/deuterium exchange MS. It concludes with a discussion of future prospects in the development of bioinformatics and potential new applications in proteomics.