A High-Throughput and In-Depth Coverage Proteomic Analysis Workflow Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry

Abstract Comprehensive proteome profiling requires improved depth and throughput, which have traditionally relied on advances in mass spectrometry (MS) and chromatographic separation. Here, we present fracSLIM, a high-throughput, deep-coverage proteomics workflow that integrates structures for lossless ion manipulation (SLIM)-based high-resolution ion mobility spectrometry–mass spectrometry (IMS-MS) with offline peptide fractionation. This approach leverages ion mobility-derived information, including enhanced separation of isomeric and isobaric species and accurate collision cross-section (CCS) measurements, to enable confident peptide identification. We evaluated the utility of this approach for complex proteomics samples by analyzing three fractions of peptide digests from human HeLa cells, enabling an over 10-fold increase in peptide identifications compared to conventional single-shot LC-MS workflows while maintaining high reproducibility. Furthermore, the workflow supports quantitative analysis by comparing endogenous peptides to heavy-isotope-labeled standards. These results highlight the potential of fracSLIM for greatly improved high-throughput and deep proteome profiling of complex samples.