Building an empirical mass spectra library for screening of organic pollutants by ultra-high-pressure liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry

Application of Nontarget High Resolution Mass Spectrometry Data to Quantitative Source Apportionment

High resolution mass spectrometry (HRMS) analyses provide expansive chemical characterizations of environmental samples. To date, most research efforts have developed tools to expedite labor- and time-intensive contaminant identification efforts. However, even without chemical identity, the richness of nontarget HRMS data sets represents a significant opportunity to chemically differentiate samples and delineate source contributions. To develop this potential, we evaluated the use of unidentified HRMS detections to define sample uniqueness and provide additional statistical resolution for quantitative source apportionment, overcoming a critical limitation of existing approaches based on targeted contaminants. By creating a series of sample mixtures that mimic pollution sources in a representative watershed, we assessed the fidelity of HRMS source fingerprints during dilution and mixing. This approach isolated 8-447 nontarget compounds per sample for source apportionment and yielded accurate source concentration estimates (between 0.82 and 1.4-fold of actual values), even in multisource systems with <1% source contributions. Furthermore, we mined the nontarget data to identify five source-specific chemical end-members amenable to apportionment. While additional development studies are needed to fully evaluate the myriad factors affecting method accuracy and capabilities, this study provides a conceptual foundation for novel applications of nontarget HRMS data to confidently distinguish and quantify source impacts in complex systems.

Secondary Metabolite Dereplication and Phylogenetic Analysis Identify Various Emerging Mycotoxins and Reveal the High Intra-Species Diversity in Aspergillus flavus

Aspergillus flavus is one of the most important mycotoxigenic species from the genus Aspergillus, due to its ability to synthesize the potent hepatocarcinogen, aflatoxin B₁. Moreover, this fungus is capable of producing several other toxic metabolites from the class of indole-tetramates, non-ribosomal peptides, and indole-diterpenoids. Populations of A. flavus are characterized by considerable diversity in terms of morphological, functional and genetic features. Although for many years A. flavus was considered an asexual fungus, researchers have shown evidence that at best these fungi can exhibit a predominantly asexual existence. We now know that A. flavus contains functional genes for mating, uncovering sexuality as potential contributor for its diversification. Based on our results, we reconfirm that A. flavus is a predominant producer of B-type aflatoxins. Moreover, this fungus can decisively produce AFM₁ and AFM₂. We did not observe any clear relationship between mating-type genes and particular class of metabolites, probably other parameters such as sexual/asexual ratio should be investigated. A dynamic secondary metabolism was found also in strains intended to be used as biocontrol agents. In addition we succeeded to provide mass spectrometry fragmentation spectra for the most important classes of A. flavus metabolites, which will serve as identification cards for future studies. Both, metabolic and phylogenetic analysis proved a high intra-species diversity for A. flavus. These findings contribute to our understanding about the diversity of Aspergillus section Flavi species, raising the necessity for polyphasic approaches (morphological, metabolic, genetic, etc.) when dealing with this type of complex group of species.

Impact of method parameters on the performance of suspect screening for the identification of trace organic contaminants in surface waters

The performance of a suspect screening method to detect diverse small-molecule trace organic contaminants (TOCs) was systematically evaluated using a set of 39 model compounds. Experiments showed that ionization efficiency, ion transfer parameters, and chromatography could affect the detection of TOCs. As expected, compounds with low ionization yields and poorly retained compounds in chromatographic columns are more difficult to identify in the samples at environmental concentrations. Similarly, TOCs with large deviations from the average mass of the compounds screened were not transmitted efficiently in the mass spectrometer thus negatively affecting their detection. The suspect screening method was validated in terms of recovery and limits of identification of the model compounds using three different types of solid-phase extraction cartridges (reversed phase with polar groups, mixed-mode anion exchange, and mixed mode cation exchange). Experiments showed that more than two-thirds of the model compounds had recoveries >75% with each of the three cartridges, and comparison of limits of identification showed that more than one-half of the model compounds could be identified at concentrations between 6 and 100 ng L−1. However, it was observed that the amount of co-extracted compounds was higher in mixed-mode ion exchangers compared with the reversed-phase cartridge. Application of the suspect screening method using the three different cartridges to surface water samples showed that between 0 to 3% of the positive matches found by the peak identification algorithm were classified as probable structures. Solutions to improve suspect screening of TOCs are proposed and discussed.

Mass spectrometric strategies for the investigation of biomarkers of illicit drug use in wastewater

The analysis of illicit drugs in urban wastewater is the basis of wastewater-based epidemiology (WBE), and has received much scientific attention because the concentrations measured can be used as a new non-intrusive tool to provide evidence-based and real-time estimates of community-wide drug consumption. Moreover, WBE allows monitoring patterns and spatial and temporal trends of drug use. Although information and expertise from other disciplines is required to refine and effectively apply WBE, analytical chemistry is the fundamental driver in this field. The use of advanced analytical techniques, commonly based on combined chromatography-mass spectrometry, is mandatory because the very low analyte concentration and the complexity of samples (raw wastewater) make quantification and identification/confirmation of illicit drug biomarkers (IDBs) troublesome. We review the most-recent literature available (mostly from the last 5 years) on the determination of IDBs in wastewater with particular emphasis on the different analytical strategies applied. The predominance of liquid chromatography coupled to tandem mass spectrometry to quantify target IDBs and the essence to produce reliable and comparable results is illustrated. Accordingly, the importance to perform inter-laboratory exercises and the need to analyze appropriate quality controls in each sample sequence is highlighted. Other crucial steps in WBE, such as sample collection and sample pre-treatment, are briefly and carefully discussed. The article further focuses on the potential of high-resolution mass spectrometry. Different approaches for target and non-target analysis are discussed, and the interest to perform experiments under laboratory-controlled conditions, as a complementary tool to investigate related compounds (e.g., minor metabolites and/or transformation products in wastewater) is treated. The article ends up with the trends and future perspectives in this field from the authors' point of view. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:258-280, 2018.

The differences in matrix effect between supercritical fluid chromatography and reversed phase liquid chromatography coupled to ESI/MS

For many sample matrices, matrix effects are a troublesome phenomenon using the electrospray ionization source. The increasing use of supercritical fluid chromatography with CO₂ in combination with the electrospray ionization source for MS detection is therefore raising questions: is the matrix effect behaving differently using SFC in comparison with reversed phase LC? This was investigated using urine, plasma, influent- and effluent-wastewater as sample matrices. The matrix effect was evaluated using the post-extraction addition method and through post-column infusions. Matrix effect profiles generated from the post-column infusions in combination with time of flight-MS detection provided the most valuable information for the study. The combination of both qualitative and semi-quantitative information with the ability to use HRMS-data for identifying interfering compounds from the same experiment was very useful, and has to the authors' knowledge not been used this way before. The results showed that both LC and SFC are affected by matrix effects, however differently depending on sample matrix. Generally, both suppressions and enhancements were seen, with a higher amount of enhancements for LC, where 65% of all compounds and all sample matrices were enhanced, compared to only 7% for SFC. Several interferences were tentatively identified, with phospholipids, creatinine, and metal ion clusters as examples of important interferences, with different impact depending on chromatographic technique. SFC needs a different strategy for limiting matrix interferences, owing to its almost reverse retention order compared to RPLC.

Behaviour of emerging contaminants in sewage sludge after anaerobic digestion

Nowadays, there is an increasing concern over the presence of contaminants in the aquatic environment, where they can be introduced from wastewater after their incomplete removal in the treatment plants. In this work, degradation of selected emerging pollutants in the aqueous and solid phases of sewage sludge has been investigated after anaerobic digestion using two different digesters: mesophilic and thermophilic. Initially, sludge samples were screened by ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF MS) for identification of emerging contaminants in the samples. In a second step, a target quantitative method based on LC coupled to tandem MS was applied for selected pollutants identified in the previous screening. The behaviour of the compounds under anaerobic conditions was studied estimating the degradation efficiency and distribution of compounds between both sludge phases. Irbesartan and benzoylecgonine seemed to be notably degraded in both phases of the sludge. Venlafaxine showed a significant concentration decrease in the aqueous phase in parallel to an increase in the solid phase. The majority of the compounds showed an increase of their concentrations in both phases after the digestion. Concentrations in the solid phase were commonly higher than in the aqueous for most contaminants, indicating that they were preferentially adsorbed onto the solid particles.

Environmental forensics in groundwater coupling passive sampling and high resolution mass spectrometry for screening

One of the difficulties encountered when monitoring groundwater quality is low and fluctuating concentration levels and complex mixtures of micropollutants, including emerging substances or transformation products. Combining passive sampling techniques with analysis by high resolution mass spectrometry (HRMS) should improve environmental metrology. Passive samplers accumulate compounds during exposure, which improves the detection of organic compounds and integrates pollution fluctuations. The Polar Organic Chemical Integrative Sampler (POCIS) were used in this study to sequester polar to semi-polar compounds. The methodology described here improves our knowledge of environmental pollution by highlighting and identifying pertinent compounds to be monitored in groundwater. The advantage of combining these two approaches is demonstrated on two different sites impacted by agricultural and/or urban pollution sources where groundwater was sampled for several months. Grab and passive sampling were done and analyzed by liquid chromatography coupled to a hybrid quadrupole time-of-flight mass spectrometer (LC-QTOF). Various data processing approaches were used (target, suspect and non-target screening). Target screening was based on research from compounds listed in a homemade database and suspect screening used a database compiled using literature data. The non-target screening was done using statistical tools such as principal components analysis (PCA) with direct connections between original chromatograms and ion intensity. Trend plots were used to highlight relevant compounds for their identification. The advantage of using POCIS to improve screening of polar organic compounds was demonstrated. Compounds undetected in water samples were detected with these tools. The subsequent data processing identified sentinel molecules, molecular clusters as compounds never revealed in these sampling sites, and molecular fingerprints. Samples were compared and multidimensional visualization of chemical patterns such as molecular fingerprints and recurrent or specific markers of each site were given.

Wide-scope screening of pesticides in fruits and vegetables using information-dependent acquisition employing UHPLC-QTOF-MS and automated MS/MS library searching

This paper presents an application of ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for simultaneous screening and identification of 427 pesticides in fresh fruit and vegetable samples. Both full MS scan mode for quantification, and an artificial-intelligence-based product ion scan mode information-dependent acquisition (IDA) providing automatic MS to MS/MS switching of product ion spectra for identification, were conducted by one injection. A home-in collision-induced-dissociation all product ions accurate mass spectra library containing more than 1700 spectra was developed prior to actual application. Both qualitative and quantitative validations of the method were carried out. The result showed that 97.4 % of the pesticides had the screening detection limit (SDL) less than 50 μg kg^-1 and more than 86.7 % could be confirmed by accurate MS/MS spectra embodied in the home-made library. Meanwhile, calibration curves covering two orders of magnitude were performed, and they were linear over the concentration range studied for the selected matrices (from 5 to 500 μg kg^-1 for most of the pesticides). Recoveries between 80 and 110 % in four matrices (apple, orange, tomato, and spinach) at two spiked levels, 10 and 100 μg kg^-1, was 88.7 or 86.8 %. Furthermore, the overall relative standard deviation (RSD, n = 12) for 94.3 % of the pesticides in 10 μg kg^-1 and 98.1 % of the pesticides in 100 μg kg^-1 spiked levels was less than 20 %. In order to validate the suitability for routine analysis, the method was applied to 448 fruit and vegetable samples purchased in different local markets. The results show 83.3 % of the analyzed samples have positive findings (higher than the limits of identification and quantification), and 412 commodity-pesticide combinations are identified in our scope. The approach proved to be a cost-effective, time-saving and powerful strategy for routine large-scope screening of pesticides.

Told through the wine: A liquid chromatography-mass spectrometry interplatform comparison reveals the influence of the global approach on the final annotated metabolites in non-targeted metabolomics

This work focuses on the influence of the selected LC-HRMS platform on the final annotated compounds in non-targeted metabolomics. Two platforms that differed in columns, mobile phases, gradients, chromatographs, mass spectrometers (Orbitrap [Platform#1] and Q-TOF [Platform#2]), data processing and marker selection protocols were compared. A total of 42 wines samples from three different protected denomination of origin (PDO) were analyzed. At the feature level, good (O)PLS-DA models were obtained for both platforms (Q(2)[Platform#1]=0.89, 0.83 and 0.72; Q(2)[Platform#2]=0.86, 0.86 and 0.77 for Penedes, Ribera del Duero and Rioja wines respectively) with 100% correctly classified samples in all cases. At the annotated metabolite level, platforms proposed 9 and 8 annotated metabolites respectively which were identified by matching standards or the MS/MS spectra of the compounds. At this stage, there was no coincidence among platforms regarding the suggested metabolites. When screened on the raw data, 6 and 5 of these compounds were detected on the other platform with a similar trend. Some of the detected metabolites showed complimentary information when integrated on biological pathways. Through the use of some examples at the annotated metabolite level, possible explanations of this initial divergence on the results are presented. This work shows the complications that may arise on the comparison of non-targeted metabolomics platforms even when metabolite focused approaches are used in the identification.

Screening of pharmaceuticals and illicit drugs in wastewater and surface waters of Spain and Italy by high resolution mass spectrometry using UHPLC-QTOF MS and LC-LTQ-Orbitrap MS

The existence of pharmaceuticals and illicit drugs (PIDs) in environmental waters has led many analytical chemists to develop screening methods for monitoring purposes. Water samples can contain a huge number of possible contaminants, commonly at low concentrations, which makes their detection and identification problematic. Liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS) has proven itself effective in the screening of environmental contaminants. The present work investigates the use of the most popular HRMS instruments, quadrupole time-of-flight and linear trap quadrupole-Orbitrap, from two different laboratories. A suspect screening for PIDs was carried out on wastewater (influent and effluent) and surface water samples from Castellón, Eastern Spain, and Cremona, Northern Italy, incorporating a database of 107 PIDs (including 220 fragment ions). A comparison between the findings of both instruments and of the samples was made which highlights the advantages and drawbacks of the strategies applied in each case. In total, 28 compounds were detected and/or identified by either/both instruments with irbesartan, valsartan, benzoylecgonine and caffeine being the most commonly found compounds across all samples.

Development of a comprehensive spectral library of sildenafil and related active analogues using LC-QTOF-MS and its application for screening counterfeit pharmaceuticals

The abuse or misuse of forged erectile-dysfunction drugs, containing phosphodiesterase type 5 inhibitors (e.g. sildenafil), is a serious issue globally. Therefore, the detection of sildenafil and related active analogues in counterfeit pharmaceuticals or the differentiation between counterfeit and authentic drugs has been performed with a variety of analytical techniques. Recently, a liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS)-based in-house library, consisting of accurate mass ion fragmentation information and retention times, was effectively applied to screen a large number of compounds in field of forensic toxicology. However, a comprehensive LC-QTOF-MS spectral library of sildenafil and related active analogues has not yet been reported. In the present study, a spectral library of 40 compounds of sildenafil and related analogues was developed with accurate mass spectra and retention times using LC-QTOF-MS, and applied to screen nine marketed counterfeit products. The in-house library successfully identified sildenafil, dimethylsildenafil, hydroxyhomosildenafil, demethylhongdenafil, pseudovardenafil and vardenafil in the samples. Our LC-QTOF-MS-based spectral library search is considered a powerful approach for identifying sildenafil and related active analogues in counterfeit pharmaceuticals.

CASMI 2013: Identification of Small Molecules by Tandem Mass Spectrometry Combined with Database and Literature Mining

The Critical Assessment of Small Molecule Identification (CASMI) contest was initiated in 2012 to evaluate manual and automated strategies for the identification of small molecules from raw mass spectrometric data. The authors participated in both category 1 (molecular formula determination) and category 2 (molecular structure determination) of the second annual CASMI contest (CASMI 2013) using slow but effective manual methods. The provided high resolution mass spectrometric data were interpreted manually using a combination of molecular formula calculators, fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic, and experience. The authors submitted correct formulas as lead candidates for 16 of 16 challenges and submitted correct structure solutions as lead candidates for 14 of 16 challenges. One structure submission (Challenge 3) was very close but not exact (N (2)-acetylglutaminylisoleucinamide instead of the correct N (2)-acetylglutaminylleucinamide). A solution for one (Challenge 13) was not submitted due to an inability to reconcile the provided fragmentation pattern with any known structures with the provided molecular composition.

Suspect screening and target quantification of multi-class pharmaceuticals in surface water based on large-volume injection liquid chromatography and time-of-flight mass spectrometry

The ever-growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight high-resolution mass spectrometry (TOF-HRMS) is a promising alternative for the state-of-the-art tandem mass spectrometry instruments because of its ability to simultaneously screen for a virtually unlimited number of suspect analytes and to perform target quantification. The challenge for such suspect screening is to develop a strategy, which minimizes the false-negative rate without restraining numerous false-positives. At the same time, omitting laborious sample enrichment through large-volume injection ultra-performance liquid chromatography (LVI-UPLC) avoids selective preconcentration. A suspect screening strategy was developed using LVI-UPLC-TOF-MS aiming the detection of 69 multi-class pharmaceuticals in surface water without the a priori availability of analytical standards. As a novel approach, the screening takes into account the signal-intensity-dependent accurate mass error of TOF-MS, hereby restraining 95 % of the measured suspect pharmaceuticals present in surface water. Application on five Belgian river water samples showed the potential of the suspect screening approach, as exemplified by a false-positive rate not higher than 15 % and given that 30 out of 37 restrained suspect compounds were confirmed by the retention time of analytical standards. Subsequently, this paper discusses the validation and applicability of the LVI-UPLC full-spectrum HRMS method for target quantification of the 69 pharmaceuticals in surface water. Analysis of five Belgian river water samples revealed the occurrence of 17 pharmaceuticals in a concentration range of 17 ng L(-1) up to 3.1 μg L(-1).

Identification of new omeprazole metabolites in wastewaters and surface waters

Omeprazole is one of the world-wide most consumed pharmaceuticals for treatment of gastric diseases. As opposed to other frequently used pharmaceuticals, omeprazole is scarcely detected in urban wastewaters and environmental waters. This was corroborated in a previous research, where parent omeprazole was not detected while four transformation products (TPs), mainly resulting from hydrolysis, were found in effluent wastewaters and surface waters. However, the low abundance of omeprazole TPs in the water samples together with the fact that omeprazole suffers an extensive metabolism, with a wide range of excretion rates (between 0.01 and 30%), suggests that human urinary metabolites should be investigated in the water environment. In this work, the results obtained in excretion tests after administration of a 40 mg omeprazole dose in three healthy volunteers are reported. Analysis by liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF MS) reported low concentrations of omeprazole in urine. Up to twenty-four omeprazole metabolites (OMs) were detected and tentatively elucidated. The most relevant OM was an omeprazole isomer, which obviously presented the same exact mass (m/z 346.1225), but also shared a major common fragment at m/z 198.0589. Subsequent analyses of surface water and effluent wastewater samples by both LC-QTOF MS and LC-MS/MS with triple quadrupole revealed that this metabolite (named as OM10) was the compound most frequently detected in water samples, followed by OM14a and OM14b. Up to our knowledge, OM10 had not been used before as urinary biomarker of omeprazole in waters. On the contrary, parent omeprazole was never detected in any of the water samples. After this research, it seems clear that monitoring the presence of omeprazole in the aquatic environment should be focused on the OMs suggested in this article instead of the parent compound.

Wide-scope analysis of pesticide and veterinary drug residues in meat matrices by high resolution MS: detection and identification using Exactive-Orbitrap

A multiresidue and multiclass method for the simultaneous determination of more than 350 compounds including pesticides, biopesticides and veterinary drugs in different meat matrices (beef, pork and chicken) by ultra-high performance liquid chromatography coupled to Orbitrap MS has been developed. In the present study, the determination of fragments was accomplished as an essential tool for a reliable identification of compounds using high resolution MS. To obtain these fragments, different strategies have been carried out in order to ensure an appropriate fragment assignment and identification. The analytical method is suitable for qualitative analysis, and it was also evaluated for quantitative analysis. Generic extraction conditions were optimized, obtaining adequate recovery and precision values for most of the studied analytes (>290). The limits of detection ranged from 2 to 16 µg kg(-1). Limits of quantification were 10 µg kg(-1) with the exception of few compounds with a higher value (50 or 100 µg kg(-1)). Limits of identification were also established, and they ranged from 2 to 150 µg kg(-1). This method was applied to the analysis of 18 meat samples and some veterinary drugs as enrofloxacin and sulfadiazine were detected and further identified/quantified (with triple quadrupole) in two different samples at 33 µg kg(-1) and trace levels, respectively. No pesticides were detected in the analyzed samples.

Investigating the presence of omeprazole in waters by liquid chromatography coupled to low and high resolution mass spectrometry: degradation experiments

Omeprazole is one of the most consumed pharmaceuticals around the world. However, this compound is scarcely detected in urban wastewater and surface water. The absence of this pharmaceutical in the aquatic ecosystem might be due to its degradation in wastewater treatment plants, as well as in receiving water. In this work, different laboratory-controlled degradation experiments have been carried out on surface water in order to elucidate generated omeprazole transformation products (TPs). Surface water spiked with omeprazole was subjected to hydrolysis, photo-degradation under both sunlight and ultraviolet radiation and chlorination. Analyses by liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF MS) permitted identification of up to 17 omeprazole TPs. In a subsequent step, the TPs identified were sought in surface water and urban wastewater by LC-QTOF MS and by LC coupled to tandem mass spectrometry with triple quadrupole. The parent omeprazole was not detected in any of the samples, but four TPs were found in several water samples. The most frequently detected compound was OTP 5 (omeprazole sulfide), which might be a reasonable candidate to be included in monitoring programs rather than the parent omeprazole.

The (un)certainty of selectivity in liquid chromatography tandem mass spectrometry

We developed a procedure to determine the "identification power" of an LC-MS/MS method operated in the MRM acquisition mode, which is related to its selectivity. The probability of any compound showing the same precursor ion, product ions, and retention time as the compound of interest is used as a measure of selectivity. This is calculated based upon empirical models constructed from three very large compound databases. Based upon the final probability estimation, additional measures to assure unambiguous identification can be taken, like the selection of different or additional product ions. The reported procedure in combination with criteria for relative ion abundances results in a powerful technique to determine the (un)certainty of the selectivity of any LC-MS/MS analysis and thus the risk of false positive results. Furthermore, the procedure is very useful as a tool to validate method selectivity.

Importance of MS selectivity and chromatographic separation in LC-MS/MS-based methods when investigating pharmaceutical metabolites in water. Dipyrone as a case of study

Pharmaceuticals are emerging contaminants of increasing concern because of their presence in the aquatic environment and potential to reach drinking-water sources. After human and/or veterinary consumption, pharmaceuticals can be excreted in unchanged form, as the parent compound, and/or as free or conjugated metabolites. Determination of most pharmaceuticals and metabolites in the environment is commonly made by liquid chromatography (LC) coupled to mass spectrometry (MS). LC coupled to tandem MS is the technique of choice nowadays in this field. The acquisition of two selected reaction monitoring (SRM) transitions together with the retention time is the most widely accepted criterion for a safe quantification and confirmation assay. However, scarce attention is normally paid to the selectivity of the selected transitions as well as to the chromatographic separation. In this work, the importance of full spectrum acquisition high-resolution MS data using a hybrid quadrupole time-of-flight analyser and/or a suitable chromatographic separation (to reduce the possibility of co-eluting interferences) is highlighted when investigating pharmaceutical metabolites that share common fragment ions. For this purpose, the analytical challenge associated to the determination of metabolites of the widely used analgesic dipyrone (also known as metamizol) in urban wastewater is discussed. Examples are given on the possibilities of reporting false positives of dypirone metabolites by LC-MS/MS under SRM mode due to a wrong assignment of identity of the compounds detected.

Qualitative aspects and validation of a screening method for pesticides in vegetables and fruits based on liquid chromatography coupled to full scan high resolution (Orbitrap) mass spectrometry

The analytical capabilities of liquid chromatography with single-stage high-resolution mass spectrometry have been investigated with emphasis on qualitative aspects related to selective detection during screening and to identification. The study involved 21 different vegetable and fruit commodities, a screening database of 556 pesticides for evaluation of false positives, and a test set of 130 pesticides spiked to the commodities at 0.01, 0.05, and 0.20 mg/kg for evaluation of false negatives. The final method involved a QuEChERS-based sample preparation (without dSPE clean up) and full scan acquisition using alternating scan events without/with fragmentation, at a resolving power of 50,000. Analyte detection was based on extraction of the exact mass (±5 ppm) of the major adduct ion at the database retention time ±30 s and the presence of a second diagnostic ion. Various options for the additional ion were investigated and compared (other adduct ions, M + 1 or M + 2 isotopes, fragments). The two-ion approach for selective detection of the pesticides in the full scan data was compared with two alternative approaches based on response thresholds. Using the two-ion approach, the number of false positives out of 11,676 pesticide/commodity combinations targeted was 36 (0.3 %). The percentage of false negatives, assessed for 2,730 pesticide/commodity combinations, was 13 %, 3 %, and 1 % at the 0.01-, 0.05-, and 0.20-mg/kg level, respectively (slightly higher with fully automated detection). Following the SANCO/12495/2011 protocol for validation of screening methods, the screening detection limit was determined for 130 pesticides and found to be 0.01, 0.05, and ≥0.20 mg/kg for 86, 30, and 14 pesticides, respectively. For the detected pesticides in the spiked samples, the ability for unambiguous identification according to EU criteria was evaluated. A proposal for adaption of the criteria was made.

Comprehensive qualitative and quantitative determination of pesticides and veterinary drugs in honey using liquid chromatography-Orbitrap high resolution mass spectrometry

A database has been created for the simultaneous analysis of more than 350 pesticides and veterinary drugs (including antibiotics) using ultra-high performance liquid chromatography coupled to high resolution Orbitrap mass spectrometry (UHPLC-Orbitrap-MS). This is a comprehensive exact mass database built using the Exactive-Orbitrap analyzer. The developed database includes exact masses of the target ions and retention time data, and allows the automatic search of the included compounds. Generic chromatographic and MS conditions have been applied. The presented database is suitable for qualitative analysis, and it was also evaluated for quantitative purposes in routine analysis, after the optimization and validation of a generic extraction method in honey samples. Adequate recovery and precision values for most of the studied analytes were obtained and the limits of detection (LOD) ranged from 1 to 50 μg kg(-1). For pesticides, LODs were always lower than the MRLs established by European Union in honey, except for a few compounds. This method was applied to the analysis of 26 real honey samples and some pesticides (azoxystrobin, coumaphos, dimethoate and thiacloprid) were detected in 4 samples. Azoxystrobin and coumaphos were determined in two different samples (organic honey) at 1.5 μg kg(-1) and 5.1 μg kg(-1). Veterinary drugs were not detected in the analyzed samples.

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis

Biological systems are increasingly being studied in a holistic manner, using omics approaches, to provide quantitative and qualitative descriptions of the diverse collection of cellular components. Among the omics approaches, metabolomics, which deals with the quantitative global profiling of small molecules or metabolites, is being used extensively to explore the dynamic response of living systems, such as organelles, cells, tissues, organs and whole organisms, under diverse physiological and pathological conditions. This technology is now used routinely in a number of applications, including basic and clinical research, agriculture, microbiology, food science, nutrition, pharmaceutical research, environmental science and the development of biofuels. Of the multiple analytical platforms available to perform such analyses, nuclear magnetic resonance and mass spectrometry have come to dominate, owing to the high resolution and large datasets that can be generated with these techniques. The large multidimensional datasets that result from such studies must be processed and analyzed to render this data meaningful. Thus, bioinformatics tools are essential for the efficient processing of huge datasets, the characterization of the detected signals, and to align multiple datasets and their features. This paper provides a state-of-the-art overview of the data processing tools available, and reviews a collection of recent reports on the topic. Data conversion, pre-processing, alignment, normalization and statistical analysis are introduced, with their advantages and disadvantages, and comparisons are made to guide the reader.

Current use of high-resolution mass spectrometry in the environmental sciences

During the last two decades, mass spectrometry (MS) has been increasingly used in the environmental sciences with the objective of investigating the presence of organic pollutants. MS has been widely coupled with chromatographic techniques, both gas chromatography (GC) and liquid chromatography (LC), because of their complementary nature when facing a broad range of organic pollutants of different polarity and volatility. A clear trend has been observed, from the very popular GC-MS with a single quadrupole mass analyser, to tandem mass spectrometry (MS-MS) and, more recently, high-resolution mass spectrometry (HRMS). For years GC has been coupled to HR magnetic sector instruments, mostly for dioxin analysis, although in the last ten years there has been growing interest in HRMS with time-of-flight (TOF) and Orbitrap mass analyzers, especially in LC-MS analysis. The increasing interest in the use of HRMS in the environmental sciences is because of its suitability for both targeted and untargeted analysis, owing to its sensitivity in full-scan acquisition mode and high mass accuracy. With the same instrument one can perform a variety of tasks: pre- and post-target analysis, retrospective analysis, discovery of metabolite and transformation products, and non-target analysis. All these functions are relevant to the environmental sciences, in which the analyst encounters thousands of different organic contaminants. Thus, wide-scope screening of environmental samples is one of the main applications of HRMS. This paper is a critical review of current use of HRMS in the environmental sciences. Needless to say, it is not the intention of the authors to summarise all contributions of HRMS in this field, as in classic descriptive reviews, but to give an overview of the main characteristics of HRMS, its strong potential in environmental mass spectrometry and the trends observed over the last few years. Most of the literature has been acquired since 2005, coinciding with the growth and popularity of HRMS in this field, with a few exceptions that deserve to be mentioned because of their relevance.

Towards a full reference library of MS(n) spectra. II: A perspective from the library of pesticide spectra extracted from the literature/Internet

To gain perspective on building full transferable libraries of MS(n) spectra from their diverse/numerous collections, a new library was built from 1723 MS(>1) spectra (mainly MS² spectra) of 490 pesticides and related compounds. Spectra acquired on different types of tandem instruments in various experimental conditions were extracted from 168 literature articles and Internet sites. Testing of the library was based on searches where 'unknown' and reference spectra originated from different sources (mainly from different laboratories) were cross-compared. The NIST 05 MS² library was added to the reference spectra. The library searches were performed with all the test spectra or were divided into different subsamples containing (a) various numbers of replicate spectra of test compounds or (b) spectra acquired from different instrument types. Thus, the dependence of true/false search (identification) result rates on different factors was explored. The percentage of 1st rank correct identifications (true positives) for the only 'unknown' mass spectrum and two and more reference spectra and matching precursor ion m/z values was 89%. For qualified matches, above the cut-off match factor, that rate decreased to 80%. The corresponding rates based on the best match for two and more 'unknown' and reference spectral replicates were 89-94%. For quadrupole instruments, the rates were even higher: 91-95% (one 'unknown' spectrum) and 90-100% (two and more such spectra). This study shows that MS² spectral libraries generated from the numerous literature/Internet sources are not less efficient for the goal of identification of unknown compounds including pesticides than very common EI-MS¹ libraries and are almost as efficient as the most productive from current MS² spectral databases. Such libraries may be used as individual reference databases or supplements to large experimental spectral collections covering many groups of abundant compounds and different types of tandem mass spectrometers.

Use of an accurate-mass database for the systematic identification of transformation products of organic contaminants in wastewater effluents

In this article, a systematic approach is proposed to assist and simplify the identification of transformation products (TPs) of organic contaminants. This approach is based on the use of characteristic fragmentation undergone by organic contaminants during MS/MS fragmentation events, and the relationship and consistency with the transformations experimented by these chemicals in the environment or during water treatment processes. With this in mind, a database containing accurate-mass information of 147 compounds and their main fragments generated by CID MS/MS fragmentation experiments was created using an LC-QTOF-MS/MS system. The developed database was applied to the identification of tentative TPs and related unexpected compounds in eight wastewater effluent samples. The approach comprises basically three stages: (a) automatic screening, (b) identification of possible TPs and (c) confirmation by MS/MS analysis. Parameters related to the search of compounds in the database have been optimized and their dependence with the exhaustiveness of the study evaluated. Eight degradation products, from the pharmaceuticals acetaminophen, amoxicillin, carbamazepine, erythromycin and azithromycin and from the pesticide diazinon, were identified with a high grade of accuracy. Three of them were confirmed by analysis of the corresponding analytical standards.