Proteomics

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


ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Colon

DISEASE(S): Colon Cancer

SUBMITTER: Ana Montero Calle  

LAB HEAD: Rodrigo Barderas

PROVIDER: PXD042597 | Pride | 2024-01-26

REPOSITORIES: Pride

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Benefits of FAIMS to Improve the Proteome Coverage of Deteriorated and/or Cross-Linked TMT 10-Plex FFPE Tissue and Plasma-Derived Exosomes Samples.

Montero-Calle Ana A   Garranzo-Asensio María M   Rejas-González Raquel R   Feliu Jaime J   Mendiola Marta M   Peláez-García Alberto A   Barderas Rodrigo R  

Proteomes 20231024 4


The proteome characterization of complex, deteriorated, or cross-linked protein mixtures as paired clinical FFPE or exosome samples isolated from low plasma volumes (250 µL) might be a challenge. In this work, we aimed at investigating 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 the analysis of protein extracts from cells, frozen tissue, and exosomes isolated from la  ...[more]

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