Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices

Photochemical and Oxidative Degradation of Chamazulene Contained in Artemisia, Matricaria and Achillea Essential Oils and Setup of Protection Strategies

Chamazulene (CA) is an intensely blue molecule with a wealth of biological properties. In cosmetics, chamazulene is exploited as a natural coloring and soothing agent. CA is unstable and tends to spontaneously degrade, accelerated by light. We studied the photodegradation of CA upon controlled exposure to UVB-UVA irradiation by multiple techniques, including GC-MS, UHPLC-PDA-ESI-MS/MS and by direct infusion in ESI-MSn, which were matched to in silico mass spectral simulations to identify degradation products. Seven byproducts formed upon UVA exposure for 3 h at 70 mW/cm2 (blue-to-green color change) were identified, including CA dimers and CA benzenoid, which were not found on extended 6 h irradiation (green-to-yellow fading). Photostability tests with reduced irradiance conducted in various solvents in the presence/absence of air indicated highest degradation in acetonitrile in the presence of oxygen, suggesting a photo-oxidative mechanism. Testing in the presence of antioxidants (tocopherol, ascorbyl palmitate, hydroxytyrosol, bakuchiol, γ-terpinene, TEMPO and their combinations) indicated the highest protection by tocopherol and TEMPO. Sunscreens ethylhexyl methoxycinnamate and particularly Tinosorb® S (but not octocrylene) showed good CA photoprotection. Thermal stability tests indicated no degradation of CA in acetonitrile at 50 °C in the dark for 50 days; however, accelerated degradation occurred in the presence of ascorbyl palmitate.

Critical Evaluation of Two Qualitative Analytical Approaches for Multiclass Determination of Veterinary Drugs in Bovine Muscle Using UHPLC-Q-Orbitrap: The Wind of Change in Brazilian Monitoring

Food safety is recognized as a main requirement for consumers, food industries, and official laboratories. Here, we present the optimization and screening qualitative validation of two multianalyte methods in bovine muscle tissues by ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry with an Orbitrap-type analyzer, operated with a heated ionization source in positive and negative mode. This aims for not only the simultaneous detection of veterinary drugs regulated in Brazil but also the prospection of antimicrobials not yet monitored. Two different sample preparation procedures were applied: method A-generic solid-liquid extraction with 0.1% formic acid (v/v) in an aqueous solution of EDTA 0.1% (w/v)-acetonitrile-methanol (1:1:1, v/v/v), followed by an additional ultrasound-assisted extraction and method B-QuEChERS. In both procedures, selectivity showed satisfactory conformity. From a detection capability (CCβ) equivalent to ½ the maximum residue limit, >34% of the analyte resulted in a false positive rate of <5%, preponderant by the QuEChERS method, which exhibited a higher yield of the sample. The results showed the potential application of both procedures in the routine analysis of foods by official laboratories, enabling the expansion of this methodological portfolio as well as its analytical scopes, thus optimizing the control of residues of veterinary drugs in the country.

Suspecting screening "known unknown" pesticides and transformation products in soil at pesticide manufacturing sites

The occurrence and risks of pesticides and their transformation products in soil at the manufacturing sites are "known unknowns." In this study, pesticides and their transformation products were screened in soil at 6 pesticide manufacturing sites across China using liquid and gas chromatography coupled with quadrupole time-of-flight mass spectrometry. The screening strategy can correctly identify 75% of 209 pesticides spiked at 50 ng g^-1. A total of 212 pesticides were identified; 23.1% of pesticides detected were above 200 ng g^-1, and the maximum concentration was 1.5 × 10⁵ ng g^-1. The risk quotients of 20% pesticides were greater than 1, and the maximum risk quotient of imidacloprid reached 6.3 × 10⁴. The most recent site showed a larger number of pesticides with higher diversity, whereas older sites were dominated by organochlorine insecticides. The extended screen identified 163 transformation products with concentrations up to 6.6 × 10⁴ ng g^-1. Half of the transformation products had higher concentrations than their parent compounds, and metabolic ratios up to 371 were observed. The results of this study validate the prevalence of pesticides and their transformation products in soil at pesticide manufacturing sites. The results also highlight the importance of comprehensive screening at industrial sites and call for improved management and regulation of pesticide manufacturing, particularly for in-service facilities.

The relevant role of ion mobility separation in LC-HRMS based screening strategies for contaminants of emerging concern in the aquatic environment

Ion mobility separation (IMS) coupled to high resolution mass spectrometry (IMS-HRMS) is a promising technique for (non-)target/suspect analysis of micropollutants in complex matrices. IMS separates ionized compounds based on their charge, shape and size facilitating the removal of co-eluting isomeric/isobaric species. Additionally, IMS data can be translated into collision cross-section (CCS) values, which can be used to increase the identification reliability. However, IMS-HRMS for the screening of contaminants of emerging concern (CECs) have been scarcely explored. In this study, the role of IMS-HRMS for the identification of CECs in complex matrices is highlighted, with emphasis on when and with which purpose is of use. The utilization of IMS can result in much cleaner mass spectra, which considerably facilitates data interpretation and the obtaining of reliable identifications. Furthermore, the robustness of IMS measurements across matrices permits the use of CCS as an additional relevant parameter during the identification step even when reference standards are not available. Moreover, an effect on the number of true and false identifications could be demonstrated by including IMS restrictions within the identification workflow. Data shown in this work is of special interest for environmental researchers dealing with the detection of CECs with state-of-the-art IMS-HRMS instruments.

Ion mobility-high resolution mass spectrometry in doping control analysis. Part II: Comparison of acquisition modes with and without ion mobility

In the second part of this study, a systematic comparison was made between two ion fragmentation acquisition modes, namely data-independent acquisition (DIA) and DIA with ion mobility spectrometry (IMS) technology. These two approaches were applied to the analysis of 192 doping agents in urine. Group I included 102 compounds such as stimulants, diuretics, narcotics, and β2-agonists, while Group II contained 90 compounds included steroids, glucocorticoids, and hormone and metabolic modulators. Important method parameters were examined and compared, including the fragmentation, sensitivity, and assignment capability with the minimum occurrence of false positive hits. The results differed between Group I and II in number of detected fragments when exploring the MS/MS spectra. In Group I only 13%, while in the Group II 64% of the substances had a higher number of fragments in DIA-IMS mode vs. DIA. In terms of sensitivity, the performance of the two modes with and without activated IMS dimension was identical for about 50% of the doping agents. The sensitivity was higher without IMS, i.e. in simple DIA mode, for 20-40% of remaining doping agents. Despite this sensitivity reduction with IMS, 82% of compounds from both Groups met the minimum required performance level (MRPL) criteria of the World Anti-Doping Agency (WADA) when the DIA-IMS mode was applied. Automated data processing is important in routine doping analysis. Therefore, processing methods were optimized and evaluated for the prevalence of false peak assignments by analysing the target substances at different concentrations in urine samples. Overall, a significantly higher number of misidentified compounds was observed in Group II, with an almost 2-fold higher number of misidentifications in DIA compared to DIA-IMS. This result highlights the benefit of the IMS dimension to reduce the rate of false positive in screening analysis. The optimized UHPLC-IM-HRMS method was finally applied to the analysis of urine samples from administration studies including nine doping agents from both Groups. However, to limit the number of interferences from the biological matrix, an emphasis is needed on the adequate settings of the data processing method.

Investigation and Resolution of Interference in the LC-QTOF-MS Detection of 4-MePPP

An interference resulting in the false-positive detection of the synthetic cathinone 4-MePPP in urine was suspected following the recent addition of 4-MePPP spectral data to an LC-QTOF-MS drug library. Although positive detection criteria were achieved, it was noted that all urine samples suspected of containing 4-MePPP also concurrently contained high levels of tramadol and its associated metabolites. Using QTOF-MS software elucidation tools, candidate compounds for the suspected interference were proposed. To provide further confidence in the identity of the interference, in silico fragmentation tools were used to match product ions generated in the analysis with product ions predicted from the theoretical fragmentation of candidate compounds. The ability of the suspected interference to subsequently produce the required product ions for spectral library identification of 4-MePPP was also tested. This information was used to provide a high preliminary confidence in the compound identity prior to purchase and subsequent confirmation with certified reference material. A co-eluting isobaric interference was identified and confirmed as an in-source fragment of the tramadol metabolite, N,N-bisdesmethyltramadol. Proposed resolutions for this interference are also described and subsequently validated by retrospective interrogation of previous cases of suspected interference.

Aptamers Which Target Proteins: What Proteotronics Suggests to Pharmaceutics

Aptamers represent a challenging field of research, relevant for diagnosis in macular degeneration, cancer, thrombosis and many inflammatory diseases, and promising in drug discovery and development. Their selection is currently performed by a stable in vitro technology, namely, SELEX. Furthermore, computationalstatistical tools have been developed to complement the SELEX selection; they work both in the preliminary stage of selection, by designing high affinity aptamers for the assigned target, and also in the final stage, analyzing the features of the best performers to implement the selection technique further. A massive use of the in silico approach is, at present, only restricted by the limited knowledge of the specific aptamer-target topology. Actually, only about fifty X-ray structures of aptamer-protein complexes have been experimentally resolved, highlighting how this knowledge has to be improved. The structure of biomolecules like aptamer-protein complexes can be represented by networks, from which several parameters can be extracted. This work briefly reviews the literature, discussing if and how general network parameters in the framework of Proteotronics and graph theory (such as electrical features, link number, free energy change, and assortativity), are important in characterizing the complexes, anticipating some features of the biomolecules. To better explain this topic, a case-study is proposed, constituted by a set of anti-angiopoietin (Ang2) aptamers, whose performances are known from the experiments, and for which two different types of conformers were predicted. A topological indicator is proposed, named Möbius (M), which combines local and global information, and seems able to discriminate between the two possible types of conformers, so that it can be considered as a useful complement to the in vitro screening for pharmaceutical aims.

Formation of Protonated ortho-Quinonimide from ortho-Iodoaniline in the Gas Phase by a Molecular-Oxygen-Mediated, ortho-Isomer-Specific Fragmentation Mechanism

Upon collisional activation under mass spectrometric conditions, protonated 2-, 3-, and 4-iodoanilines lose an iodine radical to generate primarily dehydroanilinium radical cations (m/z 93), which are the distonic counterparts of the conventional molecular ion of aniline. When briefly accumulated in the Trap region of a Triwave cell in a SYNAPT G2 instrument, before being released for ion-mobility separation, these dehydroanilinium cations react readily with traces of oxygen present in the mobility gas to form peroxyl radical cations. Although all three isomeric dehydroanilinium ions showed avid affinity for O₂, their reactivities were distinctly different. For example, the product-ion spectra recorded from mass-selected m/z 93 ion from 3- and 4-iodoanilines showed a peak at m/z 125 for the respective peroxylbenzenaminium ion. In contrast, an analogous peak at m/z 125 was absent in the spectrum of the 2-dehydroanilinium ion generated from 2-iodoaniline. Evidently, the 2-peroxylbenzenaminium ion generated from the 2-dehydroanilinium ion immediately loses a ^•OH to form protonated ortho-quinonimide (m/z 108).

Suspect, non-target and target screening of emerging pollutants using data independent acquisition: Assessment of a Mediterranean River basin

A single workflow based on three approaches (target, suspected and non-target screening) using liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (LC-QTOF-MS) in data independent acquisition mode (DIA) was developed to assess the presence of emerging pollutants (EPs) in water and sediments from a Mediterranean River Basin. Identification of potential contaminants was based on mass accuracy, isotopic ratio pattern, theoretical fragmentation, and retention time using Waters UNIFI software. In the suspect screening against a library containing 2200 components, 68 contaminants were tentatively identified, 6 of which were confirmed and quantified with analytical standards. Non-target screening (NTS) required additional manual processing and the aid of an on-line database (ChemSpider) to tentatively identify compounds. Eprosartan, an antihypertensive drug not included in the library used for suspected screening, was confirmed and semi-quantified. The identification of Eprosartan proved the workflow to be functional for NTS. Target screening of 171 pesticides and 33 pharmaceuticals and personal care products (PPCPs) including the compounds confirmed using suspect (6) and non target (1) screening achieved monitoring of the most abundant contaminants from the head to the mouth of the Turia basin to establish their spatial distribution. QTOF-MS screening versatility with its high-resolution capability allows for a comprehensive assessment of EPs in the aquatic environment.

An untargeted lipidomic approach for qualitative determination of latent fingermark glycerides using UPLC-IMS-QToF-MSE

More detailed fundamental information is required about latent fingermark composition in order to better understand fingermark properties and their impact on detection efficiency, and the physical and chemical changes that occur with time following deposition. The composition of the glyceride fraction of latent fingermark lipids in particular is relatively under-investigated due in part to their high structural variability and the limitations of the analytical methods most frequently utilised to investigate fingermark composition. Here, we present an ultra performance liquid chromatography-ion mobility spectroscopy-quadrupole time-of-flight mass spectrometry (UPLC-IMS-QToF-MS^E) method to characterise glycerides in charged latent fingermarks using data-independent acquisition. Di- and triglycerides were identified in fingermark samples from a population of 10 donors, through a combination of in silico fragmentation and monitoring for fatty acid neutral losses. 23 diglycerides and 85 families of triglycerides were identified, with significant diversity in chain length and unsaturation. 21 of the most abundant triglyceride families were found to be common to most or all donors, presenting potential targets for further studies to monitor chemical and physical changes in latent fingermarks over time. Differences in relative peak intensities may be indicative of inter- and intra-donor variability. While this study represents a promising step to obtaining more in-depth information about fingermark composition, it also highlights the complex nature of these traces.

Assessing the Quality of in Silico Produced Biomolecules: The Discovery of a New Conformer

The computational procedures for predicting the 3D structure of aptamers interacting with different biological molecules have gained increasing attention in recent years. The information acquired through these methods represents a crucial input for research, especially when relevant crystallographic data are not available. A number of software programs able to perform macromolecular docking are currently accessible, leading to the prediction of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Nevertheless, the scoring protocols employed for ranking the candidate structures do not always produce satisfactory results, making difficult the identification of structures that are most likely to occur in nature. In this paper, we propose a novel procedure to improve the predictive performances of computational scoring protocols, using a maximum likelihood estimate based on topological and electrical properties of interacting biomolecules. The reliability of the new computational approach, enabling the ranking of aptamer-protein configurations produced by an open source docking program, has been assessed by its successful application to a set of antiangiopoietin aptamers, for which experimental data highlighting the sequence-dependent affinity toward the target protein are available. The procedure led to the identification of two main types of aptamer conformers involved in angiopoietin binding. Interestingly, one of these reproduces the arrangement of angiopoietin with its natural target, tyrosine kinase, while the other one is completely unexpected. The possible scenarios related to these results have been discussed. The methodology here described can be used to refine the outcomes of different computational procedures and can be applied to a wide range of biological molecules, thus representing a new tool for guiding the design of bioinspired sensors with enhanced selectivity.

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

A new retrospective, multi-evidence veterinary drug screening method using drift tube ion mobility mass spectrometry

RATIONALE

The retrospectivity (the ability to retrospect to a previously unknown compound in raw data) is very meaningful for food safety and risk assessment when facing new emerging drugs. Accurate mass and retention time based screening may lead false positive and false negative results so new retrospective, reliable platform is desirable.

METHODS

Different concentration levels of standards with and without matrix were analyzed using ion mobility (IM)-quadrupole-time-of-flight (Q-TOF) for collecting retrospective accurate mass, retention time, drift time and tandem MS evidence for identification in a single experiment. The isomer separation ability of IM and the four-dimensional (4D) feature abundance quantification abilities were evaluated for veterinary drugs for the first time.

RESULTS

The sensitivity of the IM-Q-TOF workflow was obviously higher than that of the traditional database searching algorithm [find by formula (FbF) function] for Q-TOF. In addition, the IM-Q-TOF workflow contained most of the results from FbF and removed the false positive results. Some isomers were separated by IM and the 4D feature abundance quantitation removed interference with similar accurate mass and showed good linearity.

CONCLUSION

A new retrospective, multi-evidence platform was built for veterinary drug screening in a single experiment. The sensitivity was significantly improved and the data can be used for quantification. The platform showed its potential to be used for food safety and risk assessment.

Transformation of the gas-phase favored O-protomer of p-aminobenzoic acid to its unfavored N-protomer by ion activation in the presence of water vapor: An ion-mobility mass spectrometry study

An ion-mobility mass spectrometry study showed that the preferred O-protonated form of p-aminobenzoic in the gas phase can be converted to the thermodynamically less favored N-protomer by in-source collision-induced ion activation during the ion transfer process from the atmospheric region to the first vacuum region if the humidity is high in the ion source. Upon the addition of water vapor to the nitrogen gas used to promote the solid analyte to the gas phase under helium-plasma ionization conditions, the intensity of the ion-mobility arrival-time peak for the N-protomer increased dramatically. Evidently, the ion-activation process in the first vacuum region is able to provide the energy required to surmount the barrier to isomerize the O-protomer to the more energetic N-protomer. The transfer of the proton attached to the carbonyl oxygen atom of the O-protomer to the amino group takes place by a water-bridge mechanism. Apparently, the postionization transformations that take place during the transmission of ions from the atmospheric-pressure ion source to the detector, via different physical compartments of low to high vacuum, play an eminent role in determining the population ratios eventually manifested at the detector.