Sample preparation for proteomics and mass spectrometry from mammalian cell lines

The field of proteomics aims to investigate the cellular proteome, which plays a vital role in cell survival and function, with high sensitivity and specificity. Over the last decade, MS-based proteomics has gained attention due to advances in sample preparation methods and instrumentation as well as improved protein databases. These advancements led to the analysis of thousands of proteins in a sample and made it possible to study global protein dynamics from cell to organism level. In this chapter, we describe more recent sample preparation techniques from mammalian cell lines for MS-based proteomics: filter-aided sample preparation and in stage tip-sample preparation (using the PreOmics iST kit). In addition to these sample preparation techniques, we provided protocols related to upstream and downstream applications such as membrane fractionation, peptide fractionation, and chemical labeling, which increase the proteome coverage, improve the MS detection, and provide sample multiplexing.