plexDIA optimization

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS


Research Article Github code


Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data-independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 ( allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at

Wallmann G., Leduc A., Slavov N., Data-Driven Optimization of DIA Mass Spectrometry by DO-MS, J. Proteome Res., doi: 10.1021/acs.jproteome.3c00177; Preprint at bioRxiv doi: 10.1101/2023.02.02.526809, PDF