Optimization of cell lysis and protein digestion protocols for protein analysis by LC-MS/MS

Mass spectrometry-based proteomics is the method of choice for analyzing (sub-) proteomes from virtually any source; with cells grown in culture being the most frequently investigated samples. Using HeLa cells, we describe a strategy for the optimization of protocols for whole proteome analysis. We cover cell lysis, protein precipitation and digestion, comparing the results obtained using different parameters and offering various possibilities for the optimization of a proteomic workflow which can be used for virtually any type of animal cell grown in culture.