Assessing the performance of the Automated Sample Preparation Platform AccelerOme

One of the main issues in a proteomics experiment is sample preparation. Protocols have been designed to optimize protein extraction, digestion, enrichment, cleaning and labeling (if required). However, the whole pipeline is time consuming and concatenates a sequence of steps that might increase the analytical variability, compromising the quality of the study. The Automated Sample Preparation Platform AccelerOme from Thermo Scientific has been designed to perform a fast, automated and reproducible procedure to prepare samples for LC-MS analyses from the protein extract to the ready-to-inject mixture of TMT labeled tryptic peptides. Aiming to assess the performance of the AccelerOme platform we have performed a quantitative analysis of a reference sample consisting of a mix of three unrelated proteomes: HeLa cells, S. cerevisiae and E. coli. Samples containing four different and known proportions of the reference proteomes were compared using both, TMT isobaric labeling and label free AccelerOme protocols. Data were then evaluated to determine the trypsin digestion efficiency (0, 1, 2 and 3 missed cleavages) and reproducibility, labeling efficiency for the TMT experiment (%labeled peptides), quantitative precision and reproducibility (protein ratios across samples) and number of peptides and proteins identified under our analytical setting. Finally, results from the analysis of two independent TMT-based differential proteomics experiments will be discussed. The two experiments involve the A549-hACE2 cell line and different Listeria strains respectively, and were previously analyzed in the labusing alternative pipelines.