Evaluation of proteomics strategies for low cell numbers: SP3- and C18-based protocols combined with five cell lysis methods

New advances in the transcriptomics and flow cytometry fields have allowed the discovery of new immune cell subsets. However, most of them are extremely small populations, hampering their analysis using mass spectrometry strategies since currently these procedures are not highly efficient in small sample sizes. In this context, recent studies have improved sample processing for quantity-limited samples. Here, we aim at evaluating the combination of five cell lysis methods and two sample clean-up techniques (i.e. C18 and SP3) for the analysis of small cell numbers (2.500, 10.000, 50.000) of THP-1, differentiated THP-1 and HT-29 cell lines.