SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes.

The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.

Diffusion of interstitials in metallic systems, illustration of a complex study case: aluminum.

While diffusion mechanisms of interstitial elements in fcc systems are generally well-known, especially in the case of H atoms, we show in this work that even in the case of a simple metallic system (aluminum), the diffusion of interstitials exhibits a wide variety of paths and mechanisms that depend on the specie. We used an approach based on first-principles calculations associated with kinetic Monte-Carlo simulations and a multi-state diffusion formalism to compute the diffusion coefficients of five interstitial elements: hydrogen, boron, carbon, nitrogen and oxygen. For instance, at the atomic scale, whilst we find that C atoms prefer to be located in octahedral sites (labeled o) rather than in tetrahedral positions (labeled t), we find one additional stable position in the lattice (M). The diffusion through these three stable positions are thus studied in detail. In the case of B atoms, for which the tetrahedral site is found unstable, the diffusion path is between o-o sites. Similarly, in the case of oxygen, t positions are found to be the only stable positions (o are unstable) and the path of migration, along t-t direction, is found through a twice degenerated asymmetric transition state. In the case of H and N atoms for which t and o sites are stable, we explain why the only path is along the t-o direction. Finally, we discuss explicit formulas to compute coefficients of diffusion of interstitials in fcc structures.

Proceedings of the EuBIC Winter School 2017.

The 2017 EuBIC Winter School was held from January 10th to January 13th 2017 in Semmering, Austria. This meeting gathered international researchers in the fields of bioinformatics and proteomics to discuss current challenges in data analysis and biological interpretation. This article outlines the scientific program and exchanges that took place on this occasion and presents the current challenges of this ever-growing field. BIOLOGICAL SIGNIFICANCE: The EUPA bioinformatics community (EuBIC) organized its first winter school in January 2017. This successful event illustrates the growing need of the bioinformatics community in proteomics to gather and discuss current and future challenges in the field. In addition to the organization of yearly meetings, the young and active EuBIC community aims to develop new collaborative open source projects, spread bioinformatics knowledge in Europe, and actively promote data sharing through public repositories.