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Profiling Yeast Deletion Strains Using Sample Multiplexing and Network-Based Analyses.

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The yeast, Saccharomyces cerevisiae, is a widely used model system for investigating conserved biological functions and pathways. Advancements in sample multiplexing have facilitated the study of the yeast proteome, yet… Click to show full abstract

The yeast, Saccharomyces cerevisiae, is a widely used model system for investigating conserved biological functions and pathways. Advancements in sample multiplexing have facilitated the study of the yeast proteome, yet many yeast proteins remain uncharacterized or only partially characterized. Yeast deletion strain collections are powerful resources for yeast proteome studies, uncovering the effects of gene function, genetic interactions, and cellular stresses. As complex biological systems cannot be understood by simply analyzing the individual components, a systems approach is often required in which a protein is represented as a component of large, interacting networks. Here, we evaluate the current state of yeast proteome analysis using isobaric tag-based sample multiplexing (TMTpro16) to profile the proteomes of 75 yeast deletion strains for which we measured the abundance of nearly 5000 proteins. Using statistical approaches, we highlighted covariance and regulation subnetworks and the enrichment of gene ontology classifications for covarying and coregulated proteins. This dataset presents a resource that is amenable to further data mining to study individual deletion strains, pathways, proteins, and/or interactions thereof while serving as a template for future network-based investigations using yeast deletion strain collections.

Keywords: sample multiplexing; network based; deletion; deletion strains; yeast deletion

Journal Title: Journal of proteome research
Year Published: 2022

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