Abstract We present Slice-PASEF, a novel mass spectrometry technology based on trapped ion mobility separation of ions. Slice-PASEF allows to achieve the theoretical maximum of MS/MS sensitivity and boosts proteomics of low sample amounts. Leveraging Slice-PASEF, we show, for the first time, that comprehensive profiling of single cell-level peptide amounts is possible using ultra-fast microflow chromatography and a general-purpose mass spectrometer, allowing quantification of 1417 proteins from 200 picograms of a HeLa cell peptide standard on an Evosep One LC system coupled to a timsTOF Pro 2, at a 200 samples per day throughput. We implemented a Slice-PASEF module in our DIA-NN data processing software, to make it readily available for the proteomics community.

Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics