Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees

Abstract

A fast and memory-efficient calculation of theoretical isotope patterns is crucial for the routine interpretation of mass spectrometric data. For high-resolution experiments, calculations must procure the exact masses and probabilities of relevant isotopologues over a wide range of polyisotopic compounds, while pruning low-probable ones. Here, a novel albeit simple treelike structure is introduced to swiftly derive sets of relevant subisotopologues for each element in a molecule, which are then combined to the isotopologues of the full molecule. In contrast to existing approaches, transitions via single replacements of the most abundant isotope per element are used in separable tree branches to derive subisotopologues from each other. Moreover, the underlying transition trees prevent redundant replacements and permit the detection of the most probable isotopologue in a first phase. A relative threshold can then be exploited in a second parallelized phase for a precise prepruning of large fractions of the remaining subisotopologues. The gain in performance from such early pruning and the lower variation in the distortion of simulated data with use of relative rather than absolute thresholds were validated in a large-scale benchmark simulation, unprecedentedly comprising several thousand molecular formulas. Both the algorithm and a wealth of related features are freely available as R-package enviPat and as a user-friendly Web interface.

Role of Gold in Inflammation and Tristetraprolin Activity

“…Typical incubation times were 2hours. [24] For the titration experiment of the Zn II 2 -TTP-2D/RNA complex with Au III terpy,t he Zn II 2 -TTP-2D sample was prepared by adding two molar equivalents of zinc acetate (Zn(OAc) 2 )t o1 0mm of apo-TTP-2D in 10 mm ammonium acetate (NH 4 OAc) buffer at pH 6.9 and incubating for 30 min at 300 rpm, room temperature. The samples were directly infused at af low rate of 50-100 nL min À1 into aT hermo Scientific Orbitrap Elite mass spectrometer (Bremen, Germany) with an ano-ESI interface coupled with a2mm diameter spray tip (PicoTip, New Objective, Inc.,W oburn, MA, USA).…”

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

“…For sum formula annotations of monoisotopic peaks, the normalized isotope abundance was computed using enviPat (Loos et al, 2015) and compared with the observed normalized isotope pattern. The difference was expressed as root-mean-square-deviation in per mille (mSigma; Thiele et al, 2011).…”

Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data

“…We simulate the mass and relative intensity of the monoisotopic peak and the first five isotope peaks of six substances with enviPat [37] in centroid mode with a resolution of 10,000, namely (i) aspartic acid which has a low mass and comprises only the elements CHNO (see Table 1 for details); (ii) cysteine which has a low mass and comprises sulfur; (iii) chloramphenicol which has a low mass and comprises chlorine; (iv) digoxigenin monodigitoxoside which has a medium mass and comprises only the elements CHNO; (v) 2-Chloro-$2^{\prime }$-deoxyadenosine-$5^{\prime }$-triphosphate which has a medium mass and comprises chlorine; and (vi) autoinducer-2 which has a low mass and contains boron. The isotopic fine structure of these substances is not detectable at this resolution and hence each simulated peak is a mixture of multiple peaks from the isotopic fine structure.…”