arXiv subjects

Mateusz Krzysztof Łącki

Publications and source records attributed to Mateusz Krzysztof Łącki.

3 recordsLinked to original sources

arXiv2017

Assigning peaks and modeling ETD in top-down mass spectrometry

Among many techniques of modern mass spectrometry, the top down methods are becoming continuously more popular in the overall strive to describe the proteome. These techniques are based on fragmentation of ions inside mass spectrometers instead of being proteolytically digested. In some of these techniques, the fragmentation is induced by electron transfer. It can trigger several concurring reactions: electron transfer dissociation, electron transfer without dissociation, and proton transfer reaction. The evaluation of the extent of these reactions is important for the proper understanding of the functioning of the instrument and, what is even more important, to know if it can be used to reveal important structural information. We present a workflow for assigning peaks and interpreting the results of electron transfer driven reactions. We also present software written in Python and available under GNU v3 license.

stat.AP↗

arXiv2014

Law of Localised Fine Structure with application in mass spectrometry

This paper presents a brand new methodology to deal with isotopic fine structure calculations. By using the Poisson approximation in an entirely novel way, we introduce mathematical elegance into the discussion on the trade-off between resolution and tractability. Our considerations unify the concepts of fine-structure, equatransneutronic configurations, and aggregate isotopic structure in a natural and simple way. We show how to boost the theoretical resolution in a seemingly costless way by several orders of magnitude with respect to the already very efficient algorithms operating on isotopic aggregates. We also develop an effective new way to obtain the important peaks in the most disaggregated isotopic structure localised in a precise region in the mass domain.

physics.chem-ph↗

arXiv2014

State dependent swap strategies and adaptive adjusting of number of temperatures in Parallel Tempering algorithms

In this paper we present extensions to the original adaptive parallel tempering algorithm. Two different approaches are presented. In the first one we introduce state-dependent strategies using current information to perform a swap step. It encompasses a wide family of potential moves including the standard one and Equi Energy type move, without any loss in tractability. In the second one, we introduce online adjustment of the number of temperatures. Numerical experiments demonstrate the effectiveness of the proposed method.

stat.CO↗