The analysis of intact proteins and protein complexes presents unique challenges to mass spectrometry (MS), prompting a fundamental re-evaluation of principles previously validated for small molecules and peptides. As the initial limitations of fragmentation have largely been overcome in the past two decades—culminating in near-complete freedom of fragmentation in the latest instruments—severe...
Understanding proteins within their functional contexts, whether in tissue units, cellular neighborhoods, small clusters of cells, or even at the single-cell level, remains a significant scientific challenge that pushes the boundaries of analytical methods. Traditional proteomic approaches largely rely on antibody-based techniques, which limit multiplexing and require prior knowledge of target...
Isotope depleted protein samples have successfully addressed various challenges in native mass spectrometry (MS), notably by enhancing the signal-to-noise (S/N) ratio- an advantage particularly beneficial for high molecular weight protein analysis. In this study, we explore the broader impact of isotope depletion on reducing sample heterogeneity, and enhancing mass spectral quality in MS, as...
Conventional mass spectrometry-based proteomics use positive polarity and provide a wealth of qualitative and quantitative information; however, these methods may not capture the true complexity of the proteome. Our work aims at alleviating this issue by resorting to ionization in negative polarity to account for the acidic portion of the intact proteome that preferentially ionizes as anions....
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. In 2021, we propose GproDIA [1], a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact...
Although the characterization of intact proteins remains a demanding endeavour – particularly as protein size increases - ongoing technological/bioinformatic advancements are steadily enhancing the capabilities of top-down mass spectrometry (TDMS) for deep sequencing. Different ion activation techniques – such as electron transfer dissociation (ETD), electron transfer higher-energy collisional...
