Proteomics

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Mass spectrometry (MS)-based proteomics is commonly used to identify and quantify the hundreds to thousands of proteins that are present in complex biological samples. Widespread data sharing via publicly accessible repositories, such as PRIDE1, has now become standard practice, aided by robust user-oriented tools for data submission and inspection and bolstered by the advent of the ProteomeXchange initiative.

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most advanced methods to characterize protein complexes in plants, giving a comprehensive view on the protein-protein interactions (PPIs) of a certain protein of interest (bait). The bait protein is fused to a double affinity tag, which consists of a protein G tag and a streptavidin-binding peptide separated by a very specific protease cleavage site, allowing highly specific protein complex isolation under near-physiological conditions.

Identification of Functionally Related Enzymes by Learning-to-Rank Methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored.

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