Activity MS4Omics
Large-scale proteomics
The platform allows the characterization of complex mixtures of proteins and their relative quantification in different samples. The samples analyzed can be of different types, such as cell pellets, tissues (frozen, FFPE), organoids, spheroids, extracellular vesicles, secretomes, biological fluids, etc. Comparative analyses between samples can be performed on large cohorts.
The platform can also search for protein partners using BioID and cross-linking approaches.
Tissue imaging and profiling by mass spectrometry (MSI)
Mass spectrometry imaging (MSI) is used to obtain the spatial distribution of endogenous molecules (lipids, proteins, peptides, metabolites) or exogenous molecules (e.g. drugs) and their relative abundance on clinical or biological (animal, plant) tissue sections.
The MS4Omics platform has extensive expertise in tissue preparation (frozen or FFPE-fixed, tissue sectioning, enzymatic digestion, matrix deposition, etc.) through to MSI analysis and data reprocessing.
Several instruments are available for MSI analysis, such as the RapifleX (Bruker) and the timsTOF flex (Bruker), which allow spatial resolution down to 10 µm. Molecular mapping of tissues can be obtained using software for processing MS imaging data (FlexImaging, SCiLS Lab).
Proteogenomics and alternative proteins
The platform has expertise in identifying alternative proteins from the non-coding regions of mRNAs and non-coding RNAs. The platform has developed protocols and several bioinformatics pipelines to improve the identification of alternative proteins.
Spatially-Resolved Omics
Spatially resolved proteomics provides molecular information to be obtained at the level of a specific tissue microenvironment by performing large-scale label-free quantification and identification of proteins at a resolution of 500 µm from histological tissue sections.
This approach provides invaluable information for studying physiological or pathophysiological mechanisms and for identifying pathways that remain hidden due to dilution effects when performing whole tissue bulk proteomics. This approach can also be combined with MSI to obtain the proteome from molecularly distinct regions of tissue based on MSI images.
The platform has established a robust protocol that combines tissue microdigestion of proteins followed by their microextraction using Liquid Extraction Surface Analysis (LESA).
Interactomics
MS4Omics is also offering service in interactomics by two different approaches. The first is the cross-linking MS (XL-MS) which the platform perform from specific target after pull-down or in large-scale strategies together with the search of interactions between the reference and the alternative proteins. The second is based on proximity labelling through BioID and TurboID strategies which are performed from cells. BioID utilizes proximity-based labeling to identify proteins in close proximity to a target protein within living cells, facilitating the mapping of protein interaction networks in their native cellular context.
