Optimal Sample Preparation Workflow for Quantitative Mass Spectrometry-Based Studies in the Low Range.

Mass spectrometry (MS) enables the high-throughput characterization of thousands of proteins in one single run. Nowadays, advances in the field have allowed for deep analysis of low cell numbers, even reaching the single-cell level. However, standardized protocols are still needed in this regard, especially oriented for non-proteomics specialists. Here we detail a reproducible, easy-to-implement workflow for cell-limited sample preparation, from cell storage to peptide labelling, for further TMT-based relative quantitative MS-based analysis.