Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
Highlights
Higher organisms are composed of different cells, allowing the individual cell to specialize, and become more efficient in performing specific tasks
There are several bioorthogonal amino acids available for metabolic labeling. These amino acid analogues are either coupled to tRNA by endogenous tRNA synthetases [14,15,16,17], or by modified tRNAs synthetases [18,19,20,21] that need to be genetically transferred to the model organism or cell line of choice
The results demonstrate that successfully combined with enrichment of tagged proteins (SORT-E) is applicable for cell specific proteomics, but the authors note that tagging at different codons led to overlapping, but distinct, sets of proteomes, and suggest tagging at more than one codon for increased proteome coverage [39]
Summary
Higher organisms are composed of different cells, allowing the individual cell to specialize, and become more efficient in performing specific tasks. The coordination of biological functions requires complex signaling events, and the proteomes of cells in a heterogeneous community will differ from the proteomes of cells that are kept in monocultures. The analysis of these complex intercellular communication systems poses a significant challenge to modern cell biology and biochemistry. Methods have been developed which are capable of addressing this issue. We are focusing on the methods that have been successfully applied in the field of proteomics
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