Cross-linking/mass spectrometry is an increasingly popular approach to obtain structural information on proteins and their complexes in solution. However, methods for error assessment are under current development. We note that false-discovery rates can be estimated at different points during data analysis, and are most relevant for residue or protein pairs. Missing this point led in our exampl...

I distinguish three views, a defence of any one of which would go some way towards vindicating the view that there is something objective about the passage of time: (i) the view that the present moment is objectively distinguished; (ii) the view that time has an objective direction – that it is an objective matter which of two non-simultaneous events is the earlier and which the later; (iii) th...

Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control normally is applied to the identification process, and do ...

False vacuum decay, a quantum mechanical first-order phase transition in scalar field theories, is an important phenomenon early Universe cosmology. Recently, real-time semiclassical techniques based on ensembles of lattice simulations were applied to the problem false decay. In this context, or any other simulation, effective potential experienced by long-wavelength modes not same as bare pote...

Automated methods for assigning peptides to observed tandem mass spectra typically return a list of peptide-spectrum matches, ranked according to an arbitrary score. In this article, we describe methods for converting these arbitrary scores into more useful statistical significance measures. These methods employ a decoy sequence database as a model of the null hypothesis, and use false discover...