Enhancement of mass spectrometry performance for proteomic analyses using highfield asymmetric waveform ion mobility spectrometry (FAIMS)

Large‐scale proteomics is typically achieved using a bottom‐up approach whereby cell extracts are proteolytically digested into peptides prior to their analysis by liquid chromatography—tandem mass spectrometry (LC—MS/MS). While this strategy is largely preferred for comprehensive protein identification, the corresponding conversion of proteins to peptides significantly increases sample complexity, and typically results in tens of thousands of peptides placing considerable demands on MS instruments to obtain in‐depth proteome coverage. Current MS instrumentation enables the detection of more than 100 000 peptides in a single run, although the large majority remains inaccessible to data‐dependent LC—MS/MS. In this perspective Special Feature, Pierre Thibault and co‐workers describe the use of high‐field asymmetric waveform ion mobility spectrometry (FAIMS) and evaluate its analytical merits for proteomic applications. Pierre Thibault is Professor of Chemistry at the Université de Montréal (Montreal QC, Canada). His main research interests are in the development and implementation of new technologies in proteomics and cell biology. In multidisciplinary research, these tools provide a deeper understanding of molecular mechanisms and posttranslational modifications, which regulate the function and translocation of proteins involved in immunity and signalling in cancer cells.