Automated Isotopic Profile Deconvolution for High Resolution Mass Spectrometric Data (APGC-QToF) from Biological Matrices

Abstract

An isotopic profile matching algorithm, the isotopic profile deconvoluted chromatogram (IPDC), was developed to screen for a wide variety of organic compounds in high-resolution mass spectrometry (HRMS) data acquired from instruments with resolution power as low as 22 000 fwhm. The algorithm initiates the screening process by generating a series of C/Br/Cl/S isotopic patterns consistent with the profiles of approximately 3 million molecular formulas for compounds with potentially persistent, bioaccumulative, and toxic (PBT) properties. To evaluate this algorithm, HRMS data were screened using these seed profiles to isolate relevant chlorinated and/or brominated compounds. Data reduction techniques included mass defect filtering and retention time prediction from estimated boiling points predicted using molecular formulas and reasonable elemental conformations. A machine learning classifier was also developed using spectrometric and chromatographic variables to minimize false positives. A scoring system was developed to rank candidate molecular formulas for an isotopic feature. The IPDC algorithm was applied to a Lake Michigan lake trout extract analyzed by atmospheric pressure gas chromatography− quadrupole time-of-flight (APGC-QToF) mass spectrometry in positive and negative modes. The IPDC algorithm detected isotopic features associated with legacy contaminants and a series of unknown halogenated features. The IPDC algorithm resolved 313 and 855 halogenated features in positive and negative modes, respectively, in Lake Michigan lake trout.

IDSL.UFA assigns high confidence molecular formula annotations for untargeted LC/HRMS datasets in metabolomics and exposomics

“…A peak spacing parameter is also used to merge neighboring theoretical isotopologues depending on the HRMS instrument mass accuracy. 11 IPDBs were generated using various sources of molecular formula databases. Once, an IPDB generated, it may be reused in similar studies.…”

“…This score function is a multiplicative score function where the product of the “greater is desirable” parameters are divided by the product of the “lower is desirable” parameters to boost score values for the true candidate matches. 11 The score values should be used only to rank molecular formulas related to a peak and cannot be used to evaluate distinct peaks. Where and R 13 C IP indicate experimental and theoretical R 13 C values, respectively.…”

“…Many other successful tools have been developed to detect Br/Cl containing compounds which had a characteristics isotopic profile in the MS1 data. 11-15, 19 MFAssignR 20 can assign molecular formula using MS1 data using Kendrick mass defect combined with isotopic signatures of selected elements. But these tools were not designed and tested for large-scale human biospecimens studies which is routinely seen in the exposome research.…”

“…Among these information, molecular formula can be assigned to a LC/HRMS peak using the observed and theoretical isotopic profiles for a chemical compound. 11 Isotopic profiles are distinguishable mass spectral signature that represent atomic masses and their natural abundances in the molecular formulas of a compound. 12 Despite the known limitations of high-resolution mass spectrometry instruments, observed experimental isotopic profiles for an ionized compound may sufficiently match the theoretical counterpart within instrument errors in many instances 11, 13 , allowing to annotate LC/HRMS peaks with molecular formula 14 .…”

“…11 Isotopic profiles are distinguishable mass spectral signature that represent atomic masses and their natural abundances in the molecular formulas of a compound. 12 Despite the known limitations of high-resolution mass spectrometry instruments, observed experimental isotopic profiles for an ionized compound may sufficiently match the theoretical counterpart within instrument errors in many instances 11, 13 , allowing to annotate LC/HRMS peaks with molecular formula 14 . Peak annotation by isotopic profile matching should be performed using efficient computational strategies to account for instrumental errors, multi-sample studies, biological plausibility and chemical diversity.…”