title: IsoSpec: Hyperfast Fine Structure Calculator.
abstract: As high-resolution mass spectrometry (HRMS) becomes increasingly available, the need of software tools capable of handling more complex data is surging. The complexity of the HRMS data stems partly from the presence of isotopes that give rise to more peaks to interpret compared to lower resolution instruments. However, a new generation of fine isotope calculators is on the rise. They calculate the smallest possible sets of isotopologues. However, none of these calculators lets the user specify the joint probability of the revealed envelope in advance. Instead, the user must provide a lower limit on the probability of isotopologues of interest, that is, provide minimal peak height. The choice of such threshold is far from obvious. In particular, it is impossible to a priori balance the trade-off between the algorithm speed and the portion of the revealed theoretical spectrum. We show that this leads to considerable inefficiencies. Here, we present IsoSpec: an algorithm for fast computation of isotopologues of chemical substances that can alternate between joint probability and peak height threshold. We prove that IsoSpec is optimal in terms of time complexity. Its implementation is freely available under a 2-clause BSD license, with bindings for C++, C, R, and Python.
authors.affiliation: Department of Mathematics, Informatics, and Mechanics, University of Warsaw , 02-097 Warsaw, Poland.
authors.forename: Mateusz K
authors.identifier: 0000-0001-7415-4748
authors.initials: MK
authors.lastname: Łącki
authors.affiliation: Department of Mathematics, Informatics, and Mechanics, University of Warsaw , 02-097 Warsaw, Poland.
authors.forename: Michał
authors.initials: M
authors.lastname: Startek
authors.affiliation: Center for Proteomics, University of Antwerp , 2000 Antwerp, Belgium.|Flemish Institute for Technological Research (VITO) , 2400 Mol, Belgium.|Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University , 3500 Hasselt, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
authors.affiliation: Department of Mathematics, Informatics, and Mechanics, University of Warsaw , 02-097 Warsaw, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Gambin