An Adaptive Parallel Tempering Algorithm
Parallel tempering is a generic Markov chainMonteCarlo samplingmethod which allows good mixing with multimodal target distributions, where conventionalMetropolis- Hastings algorithms often fail. The mixing properties of the sampler depend strongly on the choice of tuning parameters, such as the temperature schedule and the proposal distribution used for local exploration. We propose an adaptive algorithm with fixed number of temperatures which tunes both the temperature schedule and the parameters of the random-walk Metropolis kernel automatically. We prove the convergence of the adaptation and a strong law of large numbers for the algorithm under general conditions. We also prove as a side…
Masstodon : a tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry
Abstract: Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites. However, several side reactions can occur under electron transfer dissociation (ETD) conditions, including nondissociative electron transfer and proton transfer reaction. Evaluating their extent can provide more insight into reaction kinetics as well as instrument operation. Furthermore, preferential formation of certain reaction products can…