The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells

Mass spectrometry-based single cell proteomics (SCP) is rapidly emerging as a powerful approach for biological research, with applications extending beyond in-vitro cancer cell lines. Recent advances make it possible to apply SCP to ex-vivo human cells from tissues such as the brain and pancreas, as well as to technically challenging immune populations such as neutrophils. However, these analyses remain more challenging and typically result in reduced proteomic coverage. To support the development of robust workflows for SCP data acquisition and analysis, we systematically evaluated multiple DIA search engines, search engine settings, the inclusion of high-load library samples in single-cell search spaces, the impact of contaminants, and the quantitative properties of identified proteins. These comparisons were performed across two major instrumentation platforms, Orbitrap Astral and timsTOF SCP, and across A549, RKO cells and neutrophils, three cell types differing in size and protein content. Our work here provides guidelines on the software parameters to use for SCP, instrument specific results and cell dependent optimizations of high-load libraries, as well as novel evaluation of the quantitative properties of proteins for single cell and low input proteomics.