An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics.

The use of protein tagging to facilitate detailed characterization of target proteins has not only revolutionized cell biology, but also enabled biochemical analysis through efficient recovery of the protein complexes wherein the tagged proteins reside. The endogenous use of these tags for detailed protein characterization is widespread in lower organisms that allow for efficient homologous recombination. With the recent advances in genome engineering, tagging of endogenous proteins is now within reach for most experimental systems, including mammalian cell lines cultures.

A decoy-free approach to the identification of peptides.

A growing number of proteogenomics and metaproteomics studies indicate potential limitations of the application of the "decoy" database paradigm used to separate correct peptide identifications from incorrect ones in traditional shotgun proteomics. We therefore propose a binary classifier called Nokoi that allows fast yet reliable decoy-free separation of correct from incorrect peptide-to-spectrum matches (PSMs). Nokoi was trained on a very large collection of heterogeneous data using ranks supplied by the Mascot search engine to label correct and incorrect PSMs.

Structure-based mutant stability predictions on proteins of unknown structure.

The ability to rapidly and accurately predict the effects of mutations on the physicochemical properties of proteins holds tremendous importance in the rational design of modified proteins for various types of industrial, environmental or pharmaceutical applications, as well as in elucidating the genetic background of complex diseases. In many cases, the absence of an experimentally resolved structure represents a major obstacle, since most currently available predictive software crucially depend on it. We investigate here the relevance of combining coarse-grained structure-based stability predictions with a simple comparative modeling procedure.

Towards a human proteomics atlas.

Proteomics research has taken up an increasingly important role in life sciences over the past few years. Due to a strong push from publishers and funders alike, the community has also started to freely share its data in earnest, making use of public repositories such as the highly popular PRIDE database at EMBL-EBI. Reuse of these publicly available data has so far been confined to rather specific, targeted reanalyses, but this limited reuse is set to expand dramatically as repositories continue to grow exponentially.