Functional and structural annotation of small proteins by advanced proteomics approaches

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We will apply proteomics approaches pioneered in our labs to discover the functional and structural context of the newly identified small proteins of Methanosarcina mazei and Salmonella typhimurium of the initial phase of SPP2002. Using protein co-expression data and machine learning we will place small proteins in the context of cellular pathways. Using co-elution analysis and in cell crosslinking mass spectrometry, methods that reveal protein-protein interactions, we will obtain a level of detail that will allow us to model their complexes. This information on the cellular pathways and structural contexts of these small proteins will guide functional experiments done by our collaborators Profs. Schmitz-Streit (M. mazei) and Erhard (S. typhimurium). Our mass spectrometric data will be shared openly through ProteomeXchange and our interaction data through our own web-based resources https://www.proteomehd.net/ and https://xiview.org/ and the widely used https://string-db.org/ (>100,000 users/week).