Metabolites rapid-annotation in mice by comprehensive method of virtual polygons and Kendric mass loss filtering: A case study of Dendrobium nobile Lindl

With significant advancements in high-resolution mass spectrometry, there has been a substantial increase in the amount of chemical component data acquired from natural products. Therefore, the rapid and efficient extraction of valuable mass spectral information from large volumes of high-resolution mass spectrometry data holds crucial significance. This study illustrates a targeted annotation of the metabolic products of alkaloid and sesquiterpene components from Dendrobium nobile (D. nobile) aqueous extract in mice serum through the integration of an in-houses database, R programming, a virtual metabolic product library, polygonal mass defect filtering, and Kendrick mass defect strategies. The research process involved initially establishing a library of alkaloids and sesquiterpenes components and simulating 71 potential metabolic reactions within the organism using R programming, thus creating a virtual metabolic product database. Subsequently, employing the virtual metabolic product library allowed for polygonal mass defect filtering, rapidly screening 1705 potential metabolites of alkaloids and 3044 potential metabolites of sesquiterpenes in the serum. Furthermore, based on the chemical composition database of D. nobile and online mass spectrometry databases, 95 compounds, including alkaloids, sesquiterpenes, and endogenous components, were characterized. Finally, utilizing Kendrick mass defect analysis in conjunction with known alkaloids and sesquiterpenes targeted screening of 209 demethylation, methylation, and oxidation products in phase I metabolism, and 146 glucuronidation and glutathione conjugation products in phase II metabolism. This study provides valuable insights for the rapid and accurate annotation of chemical components and their metabolites in vivo within natural products.

Exploring applications of non-targeted analysis in the characterization of the prenatal exposome

Capturing the breadth of chemical exposures in utero is critical in understanding their long-term health effects for mother and child. We explored methodological adaptations in a Non-Targeted Analysis (NTA) pipeline and evaluated the effects on chemical annotation and discovery for maternal and infant exposure. We focus on lesser-known/underreported chemicals in maternal and umbilical cord serum analyzed with liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). The samples were collected from a demographically diverse cohort of 296 maternal-cord pairs (n = 592) recruited in San Francisco Bay area. We developed and evaluated two data processing pipelines, primarily differing by detection frequency cut-off, to extract chemical features from non-targeted analysis (NTA). We annotated the detected chemical features by matching with EPA CompTox Chemicals Dashboard (n = 860,000 chemicals) and Human Metabolome Database (n = 3140 chemicals) and applied a Kendrick Mass Defect filter to detect homologous series. We collected fragmentation spectra (MS/MS) on a subset of serum samples and matched to an experimental MS/MS database within the MS-Dial website and other experimental MS/MS spectra collected from standards in our lab. We annotated ~72 % of the features (total features = 32,197, levels 1-4). We confirmed 22 compounds with analytical standards, tentatively identified 88 compounds with MS/MS spectra, and annotated 4862 exogenous chemicals with an in-house developed annotation algorithm. We detected 36 chemicals that appear to not have been previously reported in human blood and 9 chemicals that were reported in less than five studies. Our findings underline the importance of NTA in the discovery of lesser-known/unreported chemicals important to characterize human exposures.

Kendrick mass defect analysis - a tool for high-resolution Orbitrap mass spectrometry of native lignin

Lignin is the second most abundant biopolymer in nature and a promising renewable feedstock for the production of aromatic compounds, composite materials, sorbents, etc. Being a complex mixture of oligomeric molecules with an irregular structure, natural lignin is an extremely difficult object to study. Its molecular level characterization requires advanced analytical techniques among which atmospheric pressure photoionization Orbitrap mass spectrometry holds a promising place. In the present study, Kendrick mass defect (KMD) analysis was proposed to facilitate the visualization and interpretation of Orbitrap mass spectra of the biopolymer on an example of Siberian pine dioxane lignin preparation. The use of the typical guaiacylpropane structure C₁₀H₁₂O₄ as a Kendrick base unit made it possible to effectively identify oligomer series with different polymerization degrees and structurally related compounds, as well as to reliably determine the elemental compositions and structures of oligomers with high molecular weights (> 1 kDa). For the first time, KMD analysis was applied to the interpretation of the complex tandem mass spectra of lignin oligomers, rapid discrimination of the product ion series, and the establishment of the main collision-induced dissociation pathways. It was demonstrated that especially promising was the use of KMD filtering in the study of broadband fragmentation tandem mass spectra, which allows for the structural characterization of all oligomers with a particular degree of polymerization.

PFAS-Contaminated Soil Site in Germany: Nontarget Screening before and after Direct TOP Assay by Kendrick Mass Defect and FindPFΔS

Soil contaminations with per- and polyfluoroalkyl substances (PFAS) are of great concern due to their persistence, leading to continuous, long-term groundwater contamination. A composite sample from contaminated agricultural soil from northwestern Germany (Brilon-Scharfenberg, North Rhine-Westphalia) was investigated in depth with nontarget screening (NTS) (Kendrick mass defect and MS² fragment mass differences with FindPFΔS). Several years ago, selected PFCAs and PFSAs were identified on this site by detection in nearby surface and drinking water. We identified 10 further PFAS classes and 7 C₈-based PFAS (73 single PFAS) previously unknown in this soil including some novel PFAS. All PFAS classes except for one class comprised sulfonic acid groups and were semi-quantified with PFSA standards from which ∼97% were perfluorinated and are not expected to be degradable. New identifications made up >75% of the prior known PFAS concentration, which was estimated to >30 μg/g. Pentafluorosulfanyl (-SF₅) PFSAs are the dominant class (∼40%). Finally, the soil was oxidized with the direct TOP (dTOP) assay, revealing PFAA precursors that were covered to a large extent by identified H-containing PFAS and additional TPs (perfluoroalkyl diacids) were detected after dTOP. In this soil, however, dTOP + target analysis covers <23% of the occurring PFAS, highlighting the importance of NTS to characterize PFAS contaminations more comprehensively.

Target and Nontarget Screening of PFAS in Biosolids, Composts, and Other Organic Waste Products for Land Application in France

Zwitterionic, cationic, and anionic per- and polyfluoroalkyl substances (PFAS) are increasingly reported in terrestrial and aquatic environments, but their inputs to agricultural lands are not fully understood. Here, we characterized PFAS in 47 organic waste products (OWP) applied in agricultural fields of France, including historical and recent materials. Overall, 160 PFAS from 42 classes were detected from target screening and homologue-based nontarget screening. Target PFAS were low in agriculture-derived wastes such as pig slurry, poultry manure, or dairy cattle manure (median ∑₄₆PFAS: 0.66 μg/kg dry matter). Higher PFAS levels were reported in urban and industrial wastes, paper mill sludge, sewage sludge, or residual household waste composts (median ∑₄₆PFAS: 220 μg/kg). Historical municipal biosolids and composts (1976-1998) were dominated by perfluorooctanesulfonate (PFOS), N-ethyl perfluorooctanesulfonamido acetic acid (EtFOSAA), and cationic and zwitterionic electrochemical fluorination precursors to PFOS. Contemporaneous urban OWP (2009-2017) were rather dominated by zwitterionic fluorotelomers, which represented on average 55% of ∑₁₆₀PFAS (max: 97%). The fluorotelomer sulfonamidopropyl betaines (X:2 FTSA-PrB, median: 110 μg/kg, max: 1300 μg/kg) were the emerging class with the highest occurrence and prevalence in contemporary urban OWP. They were also detected as early as 1985. The study informs for the first time that urban sludges and composts can be a significant repository of zwitterionic and cationic PFAS.

Beyond the Tip of the Iceberg: Suspect Screening Reveals Point Source-Specific Patterns of Emerging and Novel Per- and Polyfluoroalkyl Substances in German and Chinese Rivers

Only a few dozens of the several thousand existing per- and polyfluoroalkyl substances (PFAS) are monitored using conventional target analysis. This study employed suspect screening to examine patterns of emerging and novel PFAS in German and Chinese river water affected by industrial point sources. In total, 86 PFAS were (tentatively) identified and grouped into 18 structure categories. Homologue patterns revealed distinct differences between fluoropolymer production sites of the two countries. In the Chinese Xiaoqing River Basin, the C₈ homologue was the most prevalent compound of the emerging series of chlorinated perfluoroalkyl carboxylic acids (Cl-PFCAs) and perfluoroalkylether carboxylic acids (PFECAs). In contrast, C₆ and shorter homologues were dominant in the German Alz River. This indicates that the phaseout of long-chain compounds in Europe and their ongoing production in Asian countries also apply to unregulated emerging PFAS classes. Additional characteristics to differentiate the point sources were the peak area ratio of perfluorobutane sulfonic acid (PFBS) versus the emerging compound hydro-substituted PFBS (H-PFBS) as well as the occurrence of byproducts of the sulfonated tetrafluoroethylene-based polymer Nafion. The large number of identified unregulated PFAS underlines the importance of a grouping approach on a regulatory level, whereas the revealed contamination patterns can be used to estimate, prioritize, and minimize contributions of specific sources.

PFAS Analysis with Ultrahigh Resolution 21T FT-ICR MS: Suspect and Nontargeted Screening with Unrivaled Mass Resolving Power and Accuracy

Per- and polyfluoroalkyl substances (PFASs) are a large family of thousands of chemicals, many of which have been identified using nontargeted time-of-flight and Orbitrap mass spectrometry methods. Comprehensive characterization of complex PFAS mixtures is critical to assess their environmental transport, transformation, exposure, and uptake. Because 21 tesla (T) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest available mass resolving power and sub-ppm mass errors across a wide molecular weight range, we developed a nontargeted 21 T FT-ICR MS method to screen for PFASs in an aqueous film-forming foam (AFFF) using suspect screening, a targeted formula database (C, H, Cl, F, N, O, P, S; ≤865 Da), isotopologues, and Kendrick-analogous mass difference networks (KAMDNs). False-positive PFAS identifications in a natural organic matter (NOM) sample, which served as the negative control, suggested that a minimum length of 3 should be imposed when annotating CF₂-homologous series with positive mass defects. We putatively identified 163 known PFASs during suspect screening, as well as 134 novel PFASs during nontargeted screening, including a suspected polyethoxylated perfluoroalkane sulfonamide series. This study shows that 21 T FT-ICR MS analysis can provide unique insights into complex PFAS composition and expand our understanding of PFAS chemistries in impacted matrices.

Comparative LC-MS analysis of tropolone alkaloids from in vitro cultures and native sources of Gloriosa superba by Kendrick mass defect plots

INTRODUCTION

Gloriosa superba L. is a promising antitumoural plant species as a source of colchicinoids. Ethnobotanical applications of G. superba are associated with different plant parts such as leaves, seeds, fruits, tuber and the whole plant.

OBJECTIVES

A comparative phytochemical study of purified extracts from in vitro cultures and native tubers of G. superba was carried out by ultrahigh-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HR-MS) in combination with the mass defect filtering (MDF) technique.

MATERIAL AND METHODS

The individual compounds were tentatively annotated using database correlations, retention time (Rt), accurate m/z data obtained by electrospray ionisation (ESI) (+)-HR-MS, proposed elemental composition, ring double bond equivalent (RDBeq) values and HR-MS/MS fragmentation patterns. Moreover, the identification was based on transforming the exact mass ratio (m/z) for the protonated molecular ions [М + Н]⁺ of the observed metabolites in Kendrick nominal masses (NKMs) and calculation of the Kendrick mass defect (KMD), which made it possible to graphically present the ion peaks in Kendrick plots.

RESULTS

Building Kendrick plots allows easy differentiation of small structural differences such as methylation or demethylation of compounds from the same homologous series. In this way, a wide range of tropolone alkaloids was characterised. A greater variety was observed in in vitro cultures, compared to native sources.

CONCLUSION

This LC-MS analysis unambiguously demonstrated the presence of tropolone alkaloids in in vitro cultures of G. superba. This approach of LC-MS data interpretation can be used to understand complex mass spectra such as those of plant extracts.

Dual-polarity SALDI FT-ICR MS imaging and Kendrick mass defect data filtering for lipid analysis

Lipids are biomolecules of crucial importance involved in critical biological functions. Yet, lipid content determination using mass spectrometry is still challenging due to their rich structural diversity. Preferential ionisation of the different lipid species in the positive or negative polarity is common, especially when using soft ionisation mass spectrometry techniques. Here, we demonstrate the potency of a dual-polarity approach using surface-assisted laser desorption/ionisation coupled to Fourier transform-ion cyclotron resonance (SALDI FT-ICR) mass spectrometry imaging (MSI) combined with Kendrick mass defect data filtering to (i) identify the lipids detected in both polarities from the same tissue section and (ii) show the complementarity of the dual-polarity data, both regarding the lipid coverage and the spatial distributions of the various lipids. For this purpose, we imaged the same mouse brain section in the positive and negative ionisation modes, on alternate pixels, in a SALDI FT-ICR MS imaging approach using gold nanoparticles (AuNPs) as dual-polarity nanosubstrates. Our study demonstrates, for the first time, the feasibility of (i) a dual-polarity SALDI-MSI approach on the same tissue section, (ii) using AuNPs as nanosubstrates combined with a FT-ICR mass analyser and (iii) the Kendrick mass defect data filtering applied to SALDI-MSI data. In particular, we show the complementarity in the lipids detected both in a given ionisation mode and in the two different ionisation modes. Graphical abstract.

Multistep Analysis of Diol-LC-ESI-HRMS Data Reveals Proanthocyanidin Composition of Complex Plant Extracts (PAComics)

Proanthocyanidins (PACs) are complex oligomeric or polymeric phenolic biopolymers composed of flavan-3-ol building blocks. PACs exert manifold functional bioactivities and are assessed as bioactive ingredients in a variety of food products, beverages, medicinal plants, and phytopharmaceuticals. Although analytical methods for PACs with low degree of polymerization (DP) are well established, a lack of methods for the detailed analysis of higher oligomers and polymers from complex plant extracts is obvious. For this, the present study investigated PAC-enriched extracts from four different plants, traditionally used for medical purpose (Lime flower, Hawthorn leaf and flower, Japanese Wisteria fruits without seeds, and Common Sorrel herb). PACs were separated on diol stationary-phase high-performance liquid chromatography according to the respective DP and detected by fluorescence and quadrupole time-of-flight mass spectrometry (qTOF-MS). The qTOF-MS contour plots [t_R → m/z] provided a sufficient overview on the respective PAC distribution. Subsequently, high-resolution mass spectrometry data were used for Kendrick mass defect (KMD) analysis, with (epi)catechin, the main flavan-3-ol unit in PACs, as the reference unit. The resulting KMD plots enabled an elucidation of the general polymer chain composition with regard to DP, building blocks, and potential secondary modifications (e.g., galloylation). Subsequently, analysis of MS² fragmentation patterns of PAC oligomers confirmed the structural features obtained from the KMD plots. While Lime flower contained oligomeric A- and B-type PACs, composed of (epi)catechin and (epi)afzelechin, Japanese Wisteria fruit contained PACs consisting of three different hydroxylated flavan-3-ols. Cinchonains, A-type PACs, and B-type PACs were detected in the Hawthorn plant material. Galloylated oligo- and polymeric PACs were detected in Common Sorrel herb. This multistep analysis reveals collective insights into the PAC composition of the extracts. The protocol offers a fast and reliable methodology to be used in a standard laboratory. On the other hand, this methodology reaches its limits for higher oligomeric PACs, and further optimization is necessary for a better detection of the polymers, as the optimal DP cluster detection depends on the resolution of diol stationary-phase chromatography and is therefore limited.

Development of two-dimensional gas chromatography (GC×GC) coupled with Orbitrap-technology-based mass spectrometry: Interest in the identification of biofuel composition

Comprehensive gas chromatography (GC) has emerged in recent years as the technique of choice for the analysis of volatile and semivolatile compounds in complex matrices. Coupling it with high-resolution mass spectrometry (MS) makes a powerful tool for identification and quantification of organic compounds. The results obtained in this study showed a significant improvement by using GC×GC-EI-MS in comparison with GC-EI-MS; the separation of chromatogram peaks was highly improved, which facilitated detection and identification. However, the limitation of Orbitrap mass analyzer compared with time-of-flight analyzer is the data acquisition rate; the frequency average was about 25 Hz at a mass resolving power of 15.000, which is barely sufficient for the proper reconstruction of the narrowest chromatographic peaks. On the other hand, the different spectra obtained in this study showed an average mass accuracy of about 1 ppm. Within this average mass accuracy, some reasonable elemental compositions can be proposed and combined with characteristic fragment ions, and the molecules can be identified with precision. At a mass resolving power of 7.500, the scan rate reaches 43 Hz and the GC×GC-MS peaks can be represented by more than 10 data points, which should be sufficient for quantification. The GC×GC-MS was also applied to analyze a cellulose bio-oil sample. Following this, a highly resolved chromatogram was obtained, allowing EI mass spectra containing molecular and fragment ions of many distinct molecules present in the sample to be identified.

Compositional Analysis of Heavy Petroleum Distillates by Comprehensive Two-dimensional Gas Chromatography, Field Ionization and High-resolution Mass Spectrometry

We report recent progresses of combining comprehensive two-dimensional gas chromatography (2DGC or GC × GC) separation, field ionization (FI), and time-of-flight mass spectrometry (TOF MS) for the detailed analysis of vacuum gas oil distillation (VGO) cuts. 2DGC separates petroleum molecules by the combination of boiling point and polarity. FI generates molecule ions-only mass spectra. TOF MS allows accurate mass analysis of hydrocarbon molecules. A new data analysis strategy is implemented for compositional analysis. First, all masses were separated into nominal mass classes. Since petroleum homologues have unique Kendrick mass defects (KMD), KMD plots were generated for easy recognition of homologues series within each nominal mass class. Finally, KMD windows were imposed for complete resolution of petroleum molecules. Using this approach, a total of 16 hydrocarbon types, 14 sulfur types, and their carbon number distributions were determined in the three VGO distillation cuts. Two series of geological biomarkers were also revealed by the analysis.

Pseudomonas sp. COW3 Produces New Bananamide-Type Cyclic Lipopeptides with Antimicrobial Activity against Pythium myriotylum and Pyricularia oryzae

Pseudomonas species are metabolically robust, with capacity to produce secondary metabolites including cyclic lipopeptides (CLPs). Herein we conducted a chemical analysis of a crude CLP extract from the cocoyam rhizosphere-derived biocontrol strain Pseudomonas sp. COW3. We performed in silico analyses on its whole genome, and conducted in vitro antagonistic assay using the strain and purified CLPs. Via LC-MS and NMR, we elucidated the structures of four novel members of the bananamide group, named bananamides D-G. Besides variability in fatty acid length, bananamides D-G differ from previously described bananamides A-C and MD-0066 by the presence of a serine and aspartic acid at position 6 and 2, respectively. In addition, bananamide G has valine instead of isoleucine at position 8. Kendrick mass defect (KMD) allowed the assignment of molecular formulae to bananamides D and E. We unraveled a non-ribosomal peptide synthetase cluster banA, banB and banC which encodes the novel bananamide derivatives. Furthermore, COW3 displayed antagonistic activity and mycophagy against Pythium myriotylum, while it mainly showed mycophagy on Pyricularia oryzae. Purified bananamides D-G inhibited the growth of P. myriotylum and P. oryzae and caused hyphal distortion. Our study shows the complementarity of chemical analyses and genome mining in the discovery and elucidation of novel CLPs. In addition, structurally diverse bananamides differ in their antimicrobial activity.

On the Kendrick Mass Defect Plots of Multiply Charged Polymer Ions: Splits, Misalignments, and How to Correct Them

The Kendrick mass defect (KMD) analysis of multiply charged polymeric distributions has recently revealed a surprising isotopic split in their KMD plots-namely a 1/z difference between KMDs of isotopes of an oligomer at charge state z. Relying on the KMD analysis of actual and simulated distributions of poly(ethylene oxide) (PEO), the isotopic split is mathematically accounted for and found to go with an isotopic misalignment in certain cases. It is demonstrated that the divisibility (resp. indivisibility) of the nominal mass of the repeating unit (R) by z is the condition for homolog ions to line up horizontally (resp. misaligned obliquely) in a KMD plot. Computing KMDs using a fractional base unit R/z eventually corrects the misalignments for the associated charge state while using the least common multiple of all the charge states as the divisor realigns all the points at once. The isotopic split itself can be removed by using either a new charge-dependent KMD plot compatible with any fractional base unit or the remainders of KM (RKM) recently developed for low-resolution data all found to be linked in a unified theory. These original applications of the fractional base units and the RKM plots are of importance theoretically to satisfy the basics of a mass defect analysis and practically for a correct data handling of single stage and tandem mass spectra of multiply charged homo- and copolymers. Graphical Abstract ᅟ.

Improving the Resolution of Kendrick Mass Defect Analysis for Polymer Ions with Fractional Base Units

The concept of a fractional base unit for the Kendrick mass defect (KMD) analysis of polymer ions is introduced for the first time. A fraction of the ethylene oxide (EO) repeat unit (namely EO/8) has been used for the KMD analysis of a poly(ethylene oxide) and found to amplify the variations of KMD between monoisotopic and ¹³C isotopes, producing an isotopically resolved KMD plot at full scale when the KMD plot computed with EO is fuzzy. The expansion of the KMD dimension using a fractional base unit has then been successfully used to unequivocally discriminate all the distributions from a blend of poly(ethylene oxide)s in a high resolution KMD plot calculated with EO/3 as base unit. Extending the concept of fractional base units to other repeat units, the visualization of the co-oligomers from a poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) triblock copolymer has been dramatically improved using a fraction of the propylene oxide repeat unit (namely PO/3) in an oligomer and isotope resolved plot. High resolution KMD plots were eventually calculated from tandem mass spectra of poly(dimethylsiloxane) ions using a fraction of the dimethylsiloxane (DMS) unit (namely DMS/6) with clearer point alignments and a discrimination of all the product ion series, out of reach of the KMD analysis using DMS. Versatile and producing high resolution KMD plots, the introduction of fractional base units is believed to be a major step towards the implementation of the KMD analysis as a routine data mining tool for mass spectrometry in polymer chemistry.

Comparative LC-MS-based metabolite profiling of the ancient tropical rainforest tree Symphonia globulifera

In the last few years, several phytochemical studies have been undertaken on the tropical tree Symphonia globulifera leading to the isolation and characterisation of several compounds exhibiting antiparasitic activities against Plasmodium falciparum, Trypanosoma brucei and Leishmania donovani. The comparative LC-MS based metabolite profiling study conducted on the tree led to the identification of compounds originating from specific tissues. The results showed that renewable organs/tissues can be used as the starting material for the production of polycyclic poly-prenylated-acylphloroglucinols, therefore reducing impacts on biodiversity. This study also underlined the lack of knowledge on the secondary metabolites produced by S. globulifera since only a small number of the total detected features were putatively identified using the database of known compounds for the species.