Benefits of FAIMS to improve the proteome coverage of hard-to-analyze TMT 10-plex FFPE tissue and plasma-derived exosomes samples

The analysis of complex protein mixtures, such as FFPE tissue or plasma exosomes samples, is a challenge nowadays due to the low proteome coverage achieved by mass spectrometers nowadays. We have here investigated the benefits of FAIMS technology coupled to the Orbitrap Exploris 480 mass spectrometer for the TMT quantitative proteomics analyses of these complex samples, in comparison to easy-to-work cell protein extracts. A two-hours gradient LC-MS/MS without or with FAIMS and two compensation voltages (CV=-45 and CV=-60) was used for the analysis. Although a slightly increase in the number of identified and quantified proteins was associated to a decrease in the number of identified and quantified peptides with FAIMS in the cell protein extract TMT experiment, we observed a significant improvement (>100%) in the number of peptide and protein identifications and quantifications for the plasma exosomes and FFPE tissue samples TMT experiments with FAIMS in comparison to the LC-MS/MS analysis without FAIMS. Our results highlight the potential of mass spectrometry analyses with FAIMS to increase the depth into the proteome of complex samples as FFPE and plasma-derived exosomes, which might aid in the characterization of their proteome and proteoforms and in the identification of dysregulated proteins that could be used as biomarkers.