pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information

Single -cell proteomics as an emerging field has exhibited potential in revealing cellular heterogeneity at the functional level. However, accurate interpretation of single -cell proteomics data suffers from challenges such as measurement noise, internal heterogeneity, and the limited sample size of label -free quantitative mass spectrometry. Herein, the author describes peptide -level differential expression analysis for single -cell proteomic (pepDESC), a method for detecting differentially expressed proteins using peptide -level information designed for label -free quantitative mass spectrometry -based single -cell proteomics. While, in this study, the author focuses on the heterogeneity among the limited number of samples, pepDESC is also applicable to regular -size proteomics data. By balancing proteome coverage and quantification accuracy using peptide quantification, pepDESC is demonstrated to be effective in real -world single -cell and spike -in benchmark datasets. By applying pepDESC to published single -mouse macrophage data, the author found a large fraction of differentially expressed proteins among three types of cells, which remarkably revealed distinct dynamics of different cellular functions responding to lipopolysaccharide stimulation.