Proteogenomic Analyses of Cellular Lysates Using a Phenol-Guanidinium Thiocyanate Reagent

Protein and RNA profiles are highly
informative when generating
a comprehensive understanding of the dynamics of complex biological
systems. Quantitative correlations between protein and RNA profiles
are not always high, yet simultaneous acquisition of both profiles
remains challenging, in part because of the limited availability of
samples and the inconvenience of separately preparing protein and
RNA fractions. In a previous study, protein, DNA, and RNA fractions
were simultaneously prepared from the same sample using phenol-guanidinium
isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts
in proteogenomic analyses remains poorly understood. We therefore
evaluated the performance of the P/GTC-extraction method in proteogenomic
analyses using standard HEK293-F cells and human peripheral blood
neutrophils. The latter cell type is renowned for its extreme vulnerability
to protein/RNA degradation, reflecting high protease and RNase activities.
Our data indicate that the P/GTC extraction method provides superior
protein profiles from neutrophil and HEK293-F cell samples for simultaneous
preparation of RNA and protein, as compared with those from conventional
protein extraction methods. The P/GTC extraction method therefore
provides a powerful and robust tool for a broad range of proteogenomic
studies.