Validation of the Mass-Extraction-Window for Quantitative Methods Using Liquid Chromatography High Resolution Mass Spectrometry

Distinct changes of taste quality and metabolite profile in different tomato varieties revealed by LC-MS metabolomics

Breeding of tomato varieties based on phenotypic traits can potentially lead to a decline in taste and nutritional values, thereby impacting consumer acceptance. However, taste is an intrinsic characteristic of tomatoes. Its decoding requires the identification of crucial compounds and the associated metabolic pathways implicated in taste development and formation. In this study, the taste parameter differences of four tomato varieties were distinguished using an electronic tongue. The content of organic acids and free amino acids, which were closely associated with taste variations, was quantitatively analyzed. Several important taste metabolites and metabolic pathways were identified based on LC-MS metabolomics and enrichment analysis. Through correlation analysis, it was determined that there existed significant associations between the taste, compounds, and metabolites of tomato varieties with different phenotypes. This study could provide references and theoretical basis for tomato breeding, as well as the control and evaluation of taste and quality of tomato varieties.

Simultaneous quantification of endogenous biomarkers and detection of testosterone esters in human serum using gas chromatography-high-resolution mass spectrometry

RATIONALE

High-resolution mass spectrometry (HRMS) has been demonstrated to be an alternative platform for quantitative analyses, identifying unknown compounds and gathering information for the elucidation of chemical structures. This work describes a method to detect 13 esters of testosterone (T) and 5 biomarkers in 0.1 mL of human serum using gas chromatography (GC) coupled to HRMS.

METHODS

Analytes were extracted from serum after deproteinization and liquid-liquid extraction. The trimethylsilyl derivatives were analyzed using a gas chromatograph coupled to HRMS at low electron energy to minimize molecule fragmentation. The acquisition in profiling full-scan mode was applied with a resolving power of 30 000 at m/z 400. Linearity, lower limit of quantitation, and measurement uncertainty were assessed. Precision and accuracy were assessed at 0.5 and 2 ng/mL, respectively. Mass accuracy (MA) and mass extraction window (MEW) were also evaluated.

RESULTS

T esters showed a linear response between 0.25 and 10 ng/mL (except for undecanoate, enanthate, and propionate that showed lineal responses between 0.5 and 10 ng/mL and isocaproate between 2 and 10 ng/mL); detection limits remained between 0.1 and 0.5 ng/mL and accuracy between 81% and 119%. The MA (MEW = 10 ppm) was maintained between -2.4 and 4.8 ppm. The biomarkers (T, androstenedione, dehydroepiandrosterone [DHEA], estradiol, and 17-OH-progesterone) showed a linear response within the evaluated range; quantification limits remained between 0.1 and 0.5 ng/mL (except for DHEA), the accuracy between 88% and 99%, and precision between 3.5% and 10.8%. Measurement uncertainties were found between 5.6% and 17.2%. MA (MEW = 3 ppm) was maintained between -0.47 and 0.12 ppm.

CONCLUSIONS

The method to detect T esters and five endogenous biomarkers in serum using GC coupled to HRMS showed linear responses up to 10 ng/mL with adequate precision, accuracy, and uncertainties. It was possible to distinguish cholesterol from T-isocaproate based on the MEW of 10 ppm, preventing false positives. In addition, this method allows searching for other biomarkers and/or unknown metabolites and other ester forms not included here but at a later stage if necessary.

Structural characterization and anti-oxidative activity for a glycopeptide from Ganoderma lucidum fruiting body

A water-soluble glycopeptide (named GL-PWQ3) with a molecular weight (Mw) of 2.40 × 104 g/mol was isolated from Ganoderma lucidum fruiting body by hot water extraction, membrane ultrafiltration, and gel column chromatography, which mainly consisted of glucose and galactose. Based on the methylation, FT-IR, 1D, and 2D NMR analysis, the polysaccharide portion of GL-PWQ3 was identified as a glucogalactan, which was comprised of unsubstituted (1,6-α-Galp, 1,6-β-Glcp, 1,4-β-Glcp) and monosubstituted (1,2,6-α-Galp and 1,3,6-β-Glcp) in the backbone and possible branches that at the O-3 position of 1,3-Glcp and T-Glcp, and the O-2 position of T-Fucp, T-Manp or T-Glcp. The chain conformational study by SEC-MALLS-RI and AFM revealed that GL-PWQ3 was identified as a highly branched polysaccharide with a polydispersity index of 1.25, and might have compact sphere structures caused by stacked multiple chains. Moreover, the GL-PWQ3 shows strong anti-oxidative activity in NRK-52E cells. This study provides a theoretical basis for further elucidating the structure-functionality relationships of GL-PWQ3 and its potential application as a natural antioxidant in pharmacotherapy as well as functional food additives.

Effect of cooking methods on metabolites of deep purple-fleshed sweetpotato

The effects of different cooking methods on purple-fleshed sweetpotato (PFSP) metabolites were systematically explored, containing the changes of starch, soluble sugar, volatile organic compounds and non-target metabolites after steaming, boiling and baking. Compared to raw samples, the steamed samples showed the greatest changes in starch (degraded from 53.01% to 39.5%) and soluble sugar content (increased from 11.82% to 29.08%), while the baked samples showed insignificant changes in starch (51.06%). In total, 64 volatile organic compounds were identified in PFSP, with aldehydes decreasing and terpenes increasing after cooking. However, most of them were low in content and contributed weak aroma for PFSP. More importantly, 871 non-volatile metabolites were detected in PFSP, and 83.5% of which were well-preserved after cooking, while most of the changes were concentrated in phenylpropanoids, amino acids and carbohydrates. This study enriches the understanding of quality changes after PFSP cooking and helps consumers choose the right cooking method.

An effective kinase inhibition strategy for metastatic recurrent childhood medulloblastoma

PURPOSE

Medulloblastomas (MBs) constitute the most common malignant brain tumor in children and adolescents. MYC-amplified Group 3 MBs are characterized by disease recurrence, specifically in the leptomeninges, whereby patients with these metastatic tumors have a mortality rate nearing 100%. Despite limited research on such tumors, studies on MB metastases at diagnosis suggest targeting kinases to be beneficial.

METHODS

To identify kinase inhibitors that eradicate cells driving therapy evasion and tumor dissemination, we utilized our established patient-derived xenograft (PDX) mouse-adapted therapy platform that models human MB metastatic recurrences following standard chemoradiotherapy. High-throughput screens of 640 kinase inhibitors were conducted against cells isolated from mouse spines in the PDX model and human fetal neural stem cells to reveal compounds that targeted these treatment-refractory, metastatic cells, whilst sparing healthy cells. Blood-brain barrier permeability assays and additional in vitro experimentation helped select top candidates for in vivo studies.

RESULTS

Recurrent Group 3 MB PDX spine cells were therapeutically vulnerable to a selective checkpoint kinase 1 (CHK1) inhibitor and small molecular inhibitor of platelet-derived growth factor receptor beta (PDGFRβ). Inhibitor-treated cells showed a significant reduction in MB stem cell properties associated with treatment failure. Mice also demonstrated survival advantage when treated with a CHK1 inhibitor ex vivo.

CONCLUSION

We identified CHK1 and PDGFRβ inhibitors that effectively target MB cells fueling treatment-refractory metastases. With limited research on effective therapies for Group 3 MB metastatic recurrences, this work highlights promising therapeutic options to treat these aggressive tumors. Additional studies are warranted to investigate these inhibitors' mechanisms and recommended in vivo administration.

EETs alleviate alveolar epithelial cell senescence by inhibiting endoplasmic reticulum stress through the Trim25/Keap1/Nrf2 axis

Alveolar epithelial cell (AEC) senescence is a key driver of a variety of chronic lung diseases. It remains a challenge how to alleviate AEC senescence and mitigate disease progression. Our study identified a critical role of epoxyeicosatrienoic acids (EETs), downstream metabolites of arachidonic acid (ARA) by cytochrome p450 (CYP), in alleviating AEC senescence. In vitro, we found that 14,15-EET content was significantly decreased in senescent AECs. Exogenous EETs supplementation, overexpression of CYP2J2, or inhibition of EETs degrading enzyme soluble epoxide hydrolase (sEH) to increase EETs alleviated AECs' senescence. Mechanistically, 14,15-EET promoted the expression of Trim25 to ubiquitinate and degrade Keap1 and promoted Nrf2 to enter the nucleus to exert an anti-oxidant effect, thereby inhibiting endoplasmic reticulum stress (ERS) and alleviating AEC senescence. Furthermore, in D-galactose (D-gal)-induced premature aging mouse model, inhibiting the degradation of EETs by Trifluoromethoxyphenyl propionylpiperidin urea (TPPU, an inhibitor of sEH) significantly inhibited the protein expression of p16, p21, and γH2AX. Meanwhile, TPPU reduced the degree of age-related pulmonary fibrosis in mice. Our study has confirmed that EETs are novel anti-senescence substances for AECs, providing new targets for the treatment of chronic lung diseases.

Characterization of non-volatile and volatile flavor profiles of Coregonus peled meat cooked by different methods

This study investigated the effects of different cooking methods on non-volatile flavor (free amino acids, 5'-nucleotides, and organic acids, etc.) of Coregonus peled meat. The volatile flavor characteristics were also analyzed by electric nose and gas chromatography-ion migration spectrometry (GC-IMS). The results indicated that the content of flavor substances in C. peled meat varied significantly. The electronic tongue results indicated that the richness and umami aftertaste of roasting were significantly greater. The content of sweet free amino acids, 5'-nucleotides, and organic acids was also higher in roasting group. Electronic nose principal component analysis can distinguish C. peled meat cooked (the first two components accounted for 98.50% and 0.97%, respectively). A total of 36 volatile flavor compounds were identified among different groups, including 16 aldehydes, 7 olefine aldehydes, 6 alcohols, 4 ketones, and 3 furans. In general, roasting was recommended and gave more flavor substances in C. peled meat.

Eight key rules for successful data-dependent acquisition in mass spectrometry-based metabolomics

In recent years, metabolomics has emerged as a pivotal approach for the holistic analysis of metabolites in biological systems. The rapid progress in analytical equipment, coupled to the rise of powerful data processing tools, now provides unprecedented opportunities to deepen our understanding of the relationships between biochemical processes and physiological or phenotypic conditions in living organisms. However, to obtain unbiased data coverage of hundreds or thousands of metabolites remains a challenging task. Among the panel of available analytical methods, targeted and untargeted mass spectrometry approaches are among the most commonly used. While targeted metabolomics usually relies on multiple-reaction monitoring acquisition, untargeted metabolomics use either data-independent acquisition (DIA) or data-dependent acquisition (DDA) methods. Unlike DIA, DDA offers the possibility to get real, selective MS/MS spectra and thus to improve metabolite assignment when performing untargeted metabolomics. Yet, DDA settings are more complex to establish than DIA settings, and as a result, DDA is more prone to errors in method development and application. Here, we present a tutorial which provides guidelines on how to optimize the technical parameters essential for proper DDA experiments in metabolomics applications. This tutorial is organized as a series of rules describing the impact of the different parameters on data acquisition and data quality. It is primarily intended to metabolomics users and mass spectrometrists that wish to acquire both theoretical background and practical tips for developing effective DDA methods.

Impact of different cooking methods on the flavor and chemical profile of yellow-fleshed table-stock sweetpotatoes (Ipomoea batatas L.)

This study investigated the impact of baking, boiling, and steaming on the taste, flavor, and chemical profile of yellow-fleshed sweetpotatoes (YFSP). Baked YFSP were sweeter, more palatable, and more flavorful than both steamed and boiled YFSP. Baking increased the YFSP soluble sugar content from 9.12% to 36.65%. Specifically, maltose increased by 200-fold and this possibly accounted for the sweetness of baked YFSP. From the Gas Chromatography-Mass Spectrometry analysis, the contents of furans and terpenes increased with baking, endowing baked YFSP with an aroma. On the contrary, boiling retained more carotenoids than the other cooking methods. Although cooking clearly altered YFSP, bioactive substances were predominantly preserved as only 72 out of 706 metabolites were identified as differentially accumulated metabolites between cooked and raw samples. Taken together, baked YFSP had high levels of sugars and volatile compounds, and the three cooking methods had little effect on chemical compounds. This comprehensive evaluation of cooked YFSP is a basis for sweetpotato processing and consumer choice.

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.

2020 White Paper on Recent Issues in Bioanalysis: BMV of Hybrid Assays, Acoustic MS, HRMS, Data Integrity, Endogenous Compounds, Microsampling and Microbiome (Part 1 - Recommendations on Industry/Regulators Consensus on BMV of Biotherapeutics by LCMS, Advanced Application in Hybrid Assays, Regulatory Challenges in Mass Spec, Innovation in Small Molecules, Peptides and Oligos)

The 14^th edition of the Workshop on Recent Issues in Bioanalysis (14^th WRIB) was held virtually on June 15-29, 2020 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. The 14^th WRIB included three Main Workshops, seven Specialized Workshops that together spanned 11 days in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccine. Moreover, a comprehensive vaccine assays track; an enhanced cytometry track and updated Industry/Regulators consensus on BMV of biotherapeutics by Mass Spectrometry (hybrid assays, LCMS and HRMS) were special features in 2020. As in previous years, this year's WRIB continued to gather a wide diversity of international industry opinion leaders and regulatory authority experts working on both small and large molecules to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance and achieving scientific excellence on bioanalytical issues. This 2020 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the Global Bioanalytical Community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2020 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication covers the recommendations on (Part 1) Hybrid Assays, Innovation in Small Molecules, & Regulated Bioanalysis. Part 2A (BAV, PK LBA, Flow Cytometry Validation and Cytometry Innovation), Part 2B (Regulatory Input) and Part 3 (Vaccine, Gene/Cell Therapy, NAb Harmonization and Immunogenicity) are published in volume 13 of Bioanalysis, issues 5, and 6 (2021), respectively.

Rapid quantitative screening of cyanobacteria for production of anatoxins using direct analysis in real time high-resolution mass spectrometry

RATIONALE

Anatoxins (ATXs) are a potent class of cyanobacterial neurotoxins that are increasingly problematic in drinking water reservoirs and recreational water bodies worldwide. Because of their high polarity and low molecular weight, analysis of ATXs is challenging and they can be considered underreported compared with other classes of cyanobacterial toxins. Improved screening methods are therefore needed to effectively assess their occurrence and concentrations in the environment.

METHODS

A rapid screening method was developed for ATXs in cyanobacteria using direct analysis in real time combined with high-resolution mass spectrometry (DART-HRMS), requiring less than 2 min per sample for triplicate analysis. The developed method was evaluated for its quantitative capabilities, applied to the screening of 30 cyanobacterial culture samples for the presence of anatoxin-a, homoanatoxin-a and dihydroanatoxin-a, and compared with a more typical liquid chromatography (LC)/HRMS method.

RESULTS

Excellent linearity was observed in the analysis of a matrix-matched calibration curve using DART-HRMS, with ionization suppression of about 50% and relative standard deviations between replicate analyses of approximately 30%. Limits of detection for both anatoxin-a and homoanatoxin-a were estimated as 1 ng/mL. Excellent agreement was observed between DART-HRMS and LC/HRMS with all ATX-producing cultures correctly identified and only one false positive culture by DART-HRMS.

CONCLUSIONS

DART-HRMS shows excellent promise for the rapid, quantitative screening of ATXs in cyanobacteria and could be expanded in the future to include the analysis of field samples and drinking water, as well as additional ATX analogues.

Intact mAb LC–MS for drug concentration from pre-clinical studies: bioanalytical method performance and in-life samples

Background: Antibody biotherapeutic measurement from pharmacokinetic studies has not been traditionally based on intact molecular mass as is the case for small molecules. However, recent advancements in protein capture and mass spectrometer technology have enabled intact mass detection and quantitation for dosed biotherapeutics. A bioanalytical method validation is part of the regulatory requirement for sample analysis to determine drug concentration from in-life study samples. Results/methodology: Here, an intact protein LC–MS assay is subjected to mock bioanalytical method validation, and unknown samples are compared between intact protein LC–MS and established bioanalytical assay formats: Ligand-binding assay and peptide LC–MS/MS. Discussion/conclusion: Results are presented from the intact and traditional bioanalytical method evaluations, where the in-life sample concentrations were comparable across method types with associated data analyses presented. Furthermore, for intact protein LC–MS, modification monitoring and evaluation of data processing parameters is demonstrated.

The use of UHPLC, IMS, and HRMS in multiresidue analytical methods: A critical review

Residue chemists who analyse pesticides in vegetables or veterinary drugs in animal-based food are currently facing a situation where there is a requirement to detect more and more compounds at lower and lower concentrations. Conventional tandem quadrupole instruments provide sufficient sensitivity, but speed and selectivity appear as future limitations. This will become an even larger issue when there is a need to not only detect active compounds but also their degradation products and metabolites. This will likely lead to a situation in which the conventional targeted approach must be expanded or augmented by a certain non-targeted strategy. High-resolution mass spectrometry provides such capabilities, but it frequently requires an additional degree of selectivity for the unequivocal confirmation of analytes present at trace levels in highly complex and variable food matrices. The hyphenation of ultrahigh performance liquid chromatography with ion mobility and high-resolution mass spectrometry provides analytical chemists with a new tool for performing such a demanding multiresidue analysis. The objective of this paper is to investigate the benefits of the added ion mobility dimension as well as to critically discuss the current limitations of this commercially available technology.

High-resolution mass spectrometry for bioanalytical applications: Is this the new gold standard?

Liquid chromatography coupled to quadrupole-based tandem mass spectrometry (QqQ) is termed the "gold standard" for bioanalytical applications because of its unpreceded selectivity, sensitivity, and the ruggedness of the technology. More recently, however, high-resolution mass spectrometry (HRMS) has become increasingly popular for bioanalytical applications. Nonetheless, this technique is still viewed, either as a screening technology or as a research tool. Although HRMS is actively discussed during scientific conferences, it is yet to be widely utilised in routine laboratory settings and there remains a reluctance to use HRMS for quantitative measurements in regulated environments. This paper does not aim to comprehensively describe the potential of the latest HRMS technology, but rather, it focuses on what results can be obtained and outlines the author's experiences over a period of many years of the routine application of various forms of HRMS instrumentation. Fifteen years ago, some nine different QqQ methods were used in the author's laboratory to analyse a variety of different veterinary drug resides. Today, many more analytes are quantified by seven HRMS methods and just three QqQ methods remain in use for the analysis of a small set of compounds yet to be upgraded to HRMS analysis. This continual upgrading and migration of analytical methods were accompanied by regularly participating in laboratory proficiency tests (PTs). The PT reports (covering a range of analytes and analytical methods) were used to compare the accuracy of HRMS- versus QqQ-based measurements. In the second part of this paper, the particular strengths and limitations of HRMS for both method development and routine measurements are critically discussed. This also includes some anecdotal experiences encountered when replacing QqQ assays with HRMS methods.

High-throughput quantification of carboxymethyl lysine in serum and plasma using high-resolution accurate mass Orbitrap mass spectrometry

BACKGROUND

Carboxymethyl lysine is an advanced glycation end product of interest as a potential biomarker of cardiovascular and other diseases. Available methods involve ELISA, with potential interference, or isotope dilution mass spectrometry (IDMS), with low-throughput sample preparation.

METHODS

A high-throughput sample preparation method based on 96-well plates was developed. Protein-bound carboxymethyl lysine and lysine were quantified by IDMS using reversed phase chromatography coupled to a high-resolution accurate mass Orbitrap Exactive mass spectrometer. The carboxymethyl lysine concentration (normalized to lysine concentration) was measured in 1714 plasma samples from the British Regional Heart Study (BRHS).

RESULTS

For carboxymethyl lysine, the lower limit of quantification (LLOQ) was estimated at 0.16 μM and the assay was linear between 0.25 and 10 μM. For lysine, the LLOQ was estimated at 3.79 mM, and the assay was linear between 2.5 and 100 mM. The intra-assay coefficient of variation was 17.2% for carboxymethyl lysine, 9.3% for lysine and 10.5% for normalized carboxymethyl lysine. The inter-assay coefficient of variation was 18.1% for carboxymethyl lysine, 14.8 for lysine and 16.2% for normalized carboxymethyl lysine. The median and inter-quartile range of all study samples in each batch were monitored. A mean carboxymethyl lysine concentration of 2.7 μM (IQR 2.0-3.2 μM, range 0.2-17.4 μM) and a mean normalized carboxymethyl lysine concentration of 69 μM/M lysine (IQR 54-76 μM/M, range 19-453 μM/M) were measured in the BRHS.

CONCLUSION

This high-throughput sample preparation method makes it possible to analyse large cohorts required to determine the potential of carboxymethyl lysine as a biomarker.

High-Resolution Mass Spectrometry Quantification: Impact of Differences in Data Processing of Centroid and Continuum Data

High-resolution mass spectrometry (HRMS) in full scan mode acquires all ions present in the sample of interest offering a lot of qualitative information. This, in combination with the improved performance of the new generation HRMS systems, triggers more (bio) analysts to switch from triple quad MS systems to HRMS for quantitative analysis. Quantitative processing of HRMS data is performed based on narrow mass extraction windows rather than on nominal mass product ion chromatograms (SRM or MRM). Optimal processing of HRMS data requires different considerations and software tools and can have an impact on data processing and final results. The selection of centroid versus continuum/profile data for processing, selection of the optimal narrow mass extraction window, using theoretical versus measured accurate mass for the extraction of the ion chromatograms as well as differences in calculations and data handling residing in the different vendor software packages are tackled in the presented manuscript. These differences are illustrated on HRMS data acquired for the same plasma samples on three different platforms, i.e., a Sciex QToF, a Waters QToF, and a Thermo Orbitrap system, and processed in four different software packages, i.e., Sciex Analyst® TF, Waters Masslynx, Waters Unifi, and Thermo Xcalibur. The impact of these differences on quantitative HRMS performance was evaluated on calibration curves of eight small molecule compounds in plasma using four different ways of processing. Simple guidelines are provided for the selection of an optimal mass extraction window for continuum and centroided data. Graphical Abstract.

Selectivity enhancement using sequential mass isolation window acquisition with hybrid quadrupole time-of-flight mass spectrometry for pesticide residues

The introduction of sequential mass isolation window acquisition mode in high-resolution quadrupole time-of-flight analysers undoubtedly represents an important improvement in the MS/MS spectra obtained when working in non-target analysis. However, the advantages and limitations of this approach have not been sufficiently defined and evaluated. The present work seeks to fill this gap by considering its application in non-target multiresidue pesticide analysis. This work focuses on the called SWATH^® method, which combines both MS and MS/MS acquisition, dividing the entire mass range into smaller segments for the MS/MS mode. The effect of the number of mass isolation windows, the total cycle-time lapsed, the sensitivity obtained, the MS/MS spectra quality, the ion ratio stability as well as the identification and quantification capabilities has been evaluated. The use of ten mass isolation windows for data acquisition was selected as a compromise between the required points per chromatographic peak and the reduction in interferences achieved. An identification study was carried out on 141 pesticides in 20 vegetable matrices to check the false positives and false identifications found automatically, in accordance with the criteria set out in Document No. SANTE/11945/2015. Furthermore, special attention was given to certain issues that can make correct identification difficult, such as low fragment abundance due using of a generic collision energy, the matrix influence on the collision cell, the effect of the concentration level as well as deconvolution failure and mass window width. Finally, to verify the efficiency of the optimum parameters proposed, two proficiency samples were analysed, obtaining good results. This proved the benefits in terms of identification and quantification purposes.

Ultra-Performance Liquid Chromatography-High-Resolution Mass Spectrometry and Direct Infusion-High-Resolution Mass Spectrometry for Combined Exploratory and Targeted Metabolic Profiling of Human Urine

The application of metabolic phenotyping to epidemiological studies involving thousands of biofluid samples presents a challenge for the selection of analytical platforms that meet the requirements of high-throughput precision analysis and cost-effectiveness. Here direct infusion–nanoelectrospray (DI–nESI) was compared with an ultra-performance liquid chromatography (UPLC)–high-resolution mass spectrometry (HRMS) method for metabolic profiling of an exemplary set of 132 human urine samples from a large epidemiological cohort. Both methods were developed and optimized to allow the simultaneous collection of high-resolution urinary metabolic profiles and quantitative data for a selected panel of 35 metabolites. The total run time for measuring the sample set in both polarities by UPLC–HRMS was 5 days compared with 9 h by DI–nESI–HRMS. To compare the classification ability of the two MS methods, we performed exploratory analysis of the full-scan HRMS profiles to detect sex-related differences in biochemical composition. Although metabolite identification is less specific in DI–nESI–HRMS, the significant features responsible for discrimination between sexes were mostly the same in both MS-based platforms. Using the quantitative data, we showed that 10 metabolites have strong correlation (Pearson’s r > 0.9 and Passing–Bablok regression slope of 0.8–1.3) and good agreement assessed by Bland–Altman plots between UPLC–HRMS and DI–nESI–HRMS and thus can be measured using a cheaper and less sample- and time-consuming method. A further twenty metabolites showed acceptable correlation between the two methods with only five metabolites showing weak correlation (Pearson’s r < 0.4) and poor agreement due to the overestimation of the results by DI–nESI–HRMS. 

Fully-automated systems and the need for global approaches should exhort clinical labs to reinvent routine MS analysis?

Today, many LC–high-resolution MS instruments have become affordable, easy-to-use, sensitive and quantitative. Meanwhile, there is an increased need for more comprehensive approaches. However, omics analyses are still restricted to specialists whereas, in hospitals, routine analyses are targeted and quantitative and represent the main and heavy tasks. But the availability of fully automated LC–MS instruments that can handle independently from sample extraction to result reporting, as well as the increasing biomedical interest for global approaches, clinical analytical workflow should be reorganized. Bioanalysts are now in the position to develop/implement clinical metabolomics or proteomics as routine analyses. In this article, this coming evolution and the reasons to implement global/omics determinations as routine analysis, is described.

Data-Independent Mass Spectrometry Approach for Screening and Identification of DNA Adducts

Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MSn) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer. An "untargeted" method is required that captures global exposures to chemicals, by simultaneously detecting their DNA adducts in the genome; some of which may induce cancer-causing mutations. We established a wide selected ion monitoring tandem mass spectrometry (wide-SIM/MS2) screening method utilizing ultraperformance-LC nanoelectrospray ionization Orbitrap MSn with online trapping to enrich bulky, nonpolar adducts. Wide-SIM scan events are followed by MS2 scans to screen for modified nucleosides by coeluting peaks containing precursor and fragment ions differing by -116.0473 Da, attributed to the neutral loss of deoxyribose. Wide-SIM/MS2 was shown to be superior in sensitivity, specificity, and breadth of adduct coverage to other tested adductomic methods with detection possible at adduct levels as low as 4 per 109 nucleotides. Wide-SIM/MS2 data can be analyzed in a "targeted" fashion by generation of extracted ion chromatograms or in an "untargeted" fashion where a chromatographic peak-picking algorithm can be used to detect putative DNA adducts. Wide-SIM/MS2 successfully detected DNA adducts, derived from chemicals in the diet and traditional medicines and from lipid peroxidation products, in human prostate and renal specimens.

Development and validation of an ultra performance liquid chromatography Q-Exactive Orbitrap mass spectrometry for the determination of fipronil and its metabolites in tea and chrysanthemum

A fast, sensitive and reliable method for the determination of fipronil and its metabolites in tea and chrysanthemum was developed using a modified QuEChERS technique and an ultra performance liquid chromatography Q-Exactive Orbitrap mass spectrometry. The mixture of adsorbents containing primary secondary amine (PSA), octadecylsilane (C₁₈) and carbon nanotubes (CNTs), was used as QuEChERS adsorbents. The use of mass resolution at 70000 full width at half maximum (FWHM) and narrow mass windows at 5 ppm achieved high selectivity and repeatability. Satisfactory linearity with correlative coefficient (R²) higher than 0.996 was achieved for all compounds. Recoveries at three levels (2, 10 and 50 μg kg^-1) ranged from 86% to 112%, while the intra- and inter-day accuracies were less than 15%. Limits of quantification for fipronil and its metabolites were 2 μg kg^-1, which fulfils the requirement of maximum residue limits formulated by European Union and Japan.

Database-driven screening of South African surface water and the targeted detection of pharmaceuticals using liquid chromatography - High resolution mass spectrometry

Pharmaceuticals and personal care products are released into aquatic environments, largely as a result of ineffectual removal during wastewater treatment. Here we present a screening strategy based on the use of three commercially available mass spectral databases, combined into a single searchable entity and parallelized by cluster computing. In addition to this, a targeted solid phase extraction method with Ultra High Pressure Liquid Chromatography coupled to quadrupole time of flight mass spectrometry (UHPLC-QTOF) was used to quantify 99 pharmaceuticals in South African surface water on a national level. Limits of quantification were in the low ng/L range for the majority of the compounds and it was found that nationally both Lamotrigine and Nevirapine occurred most often. Prednisolone and Ritonavir were present at the highest average concentration; 623 and 489 ng/L respectively. It is however shown that more than 50% of the targets chosen for analysis are not detectable in any of the samples, which highlights the utility of untargeted, database driven screening; prior to the use of costly analytical standards. Untargeted screening detected 45% of the compounds detected in targeted mode, and furthermore tentatively identified a total of 4273 unique compounds across the samples. Automatically triggered MS/MS analyses yielded 92 unique hits with greater than 95% confidence. It is therefore suggested that untargeted screening should precede the targeted approach as a matter of economy and to guide the selection of targets for quantification. There is however great room for improvement in current commercial database search methodologies as a large bottleneck exists due to processing time.

Quantification of steroid hormones in human serum by liquid chromatography-high resolution tandem mass spectrometry

A limited specificity is inherent to immunoassays for steroid hormone analysis. To improve selectivity mass spectrometric analysis of steroid hormones by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been introduced in the clinical laboratory over the past years usually with low mass resolution triple-quadrupole instruments or more recently by high resolution mass spectrometry (HR-MS). Here we introduce liquid chromatography-high resolution tandem mass spectrometry (LC-MS/HR-MS) to further increase selectivity of steroid hormone quantification. Application of HR-MS demonstrates an enhanced selectivity compared to low mass resolution. Separation of isobaric interferences reduces background noise and avoids overestimation. Samples were prepared by automated liquid-liquid extraction with MTBE. The LC-MS/HR-MS method using a quadrupole-Orbitrap analyzer includes eight steroid hormones i.e. androstenedione, corticosterone, cortisol, cortisone, 11-deoxycortisol, 17-hydroxyprogesterone, progesterone, and testosterone. It has a run-time of 5.3min and was validated according to the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA) guidelines. For most of the analytes coefficient of variation were 10% or lower and LOQs were determined significantly below 1ng/ml. Full product ion spectra including accurate masses substantiate compound identification by matching their masses and ratios with authentic standards. In summary, quantification of steroid hormones by LC-MS/HR-MS is applicable for clinical diagnostics and holds also promise for highly selective quantification of other small molecules.

Sensitive and selective quantification of free and total malondialdehyde in plasma using UHPLC-HRMS

Quantification of malondialdehyde (MDA) as a marker of lipid peroxidation is relevant for many research fields. We describe a new sensitive and selective method to measure free and total plasmatic MDA using derivatization with 2,4-dinitrophenylhydrazine (DNPH) and ultra-HPLC-high-resolution MS. Free and total MDA were extracted from minute sample amounts (10 μl) using acidic precipitation and alkaline hydrolysis followed by acidic precipitation, respectively. Derivatization was completed within 10 min at room temperature, and the excess DNPH discarded by liquid-liquid extraction. Quantification was achieved by internal standardization using dideuterated MDA as internal standard. The method's lowest limit of quantification was 100 nM and linearity spanned greater than three orders of magnitude. Intra- and inter-day precisions for total MDA were 2.9% and 3.0%, respectively, and those for free MDA were 12.8% and 24.9%, respectively. Accuracy was 101% and 107% at low and high concentrations, respectively. In human plasma, free MDA levels were 120 nM (SD 36.26) and total MDA levels were 6.7 μM (SD 0.46). In addition, we show the applicability of this method to measure MDA plasma levels from a variety of animal species, making it invaluable to scientists in various fields.

Biomonitoring DNA Adducts of Cooked Meat Carcinogens in Human Prostate by Nano Liquid Chromatography-High Resolution Tandem Mass Spectrometry: Identification of 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine DNA Adduct

Epidemiologic studies have reported an association between frequent consumption of well-done cooked meats and prostate cancer risk. However, unambiguous physiochemical markers of DNA damage from carcinogens derived from cooked meats, such as DNA adducts, have not been identified in human samples to support this paradigm. We have developed a highly sensitive nano-LC-Orbitrap MS n method to measure DNA adducts of several carcinogens originating from well-done cooked meats, tobacco smoke, and environmental pollution, including 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-9H-pyrido[2,3-b]indole (AαC), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), benzo[a]pyrene (B[a]P), and 4-aminobiphenyl (4-ABP). The limit of quantification (LOQ) of the major deoxyguanosine (dG) adducts of these carcinogens ranged between 1.3 and 2.2 adducts per 10 9 nucleotides per 2.5 μg of DNA assayed. The DNA adduct of PhIP, N-(deoxyguanosin-8-yl)-PhIP (dG-C8-PhIP) was identified in 11 out of 35 patients, at levels ranging from 2 to 120 adducts per 10 9 nucleotides. The dG-C8 adducts of AαC and MeIQx, and the B[a]P adduct, 10-(deoxyguanosin-N 2 -yl)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[a]pyrene (dG-N 2 -B[a]PDE) were not detected in any specimen, whereas N-(deoxyguanosin-8-yl)-4-ABP (dG-C8-4-ABP) was identified in one subject (30 adducts per 10 9 nucleotides). PhIP-DNA adducts also were recovered quantitatively from formalin fixed paraffin embedded (FFPE) tissues, signifying FFPE tissues can serve as biospecimens for carcinogen DNA adduct biomarker research. Our biomarker data provide support to the epidemiological observations implicating PhIP, one of the most mass-abundant heterocyclic aromatic amines formed in well-done cooked meats, as a DNA-damaging agent that may contribute to the etiology of prostate cancer.

Unconjugated payload quantification and DAR characterization of antibody–drug conjugates using high-resolution MS

Aim: The application of high-resolution MS to antibody–drug conjugate (ADC) drug development may provide insight into their safety and efficacy. Quantification of unconjugated cytotoxic drug (payload) and characterization of drug-to-antibody ratio distribution were determined in plasma using orthogonal acceleration quadrupole-time-of-flight MS. Results: Unconjugated payload quantification determined by quadrupole-time-of-flight-based MRMhighresolution and triple quadrupole-based multiple reaction monitoring were comparable and achieved detection limits of 0.030 and 0.015 ng/ml, respectively. As determined by immunocapture and TOF-MS, drug-to-antibody ratio remained unchanged up to 3-weeks postdose for an ADC containing engineered glutamine linkers, but declined from four to three over 2 weeks in an ADC containing engineered cysteine linkers. Conclusion: The use of high-resolution MS in ADC drug discovery confirms its utility within the bioanalytical discipline.

HRMS using a Q-Exactive series mass spectrometer for regulated quantitative bioanalysis: how, when, and why to implement

High-resolution MS (HRMS) has seen an uptake in use for discovery qual/quan workflows, however, its utilization in late discovery/development has been slow. Past reports comparing HRMS to triple quadrupole (QQQ) instrumentation to date have indicated that HRMS instruments are capable of producing data acceptable for regulated bioanalysis, however lack the sensitivity required for sub ng/ml LLOQ assays. Recent advances in HRMS instrumentation have closed the sensitivity gap with QQQ and have even provided improved selectivity and sensitivity over QQQ SRM assays. Herein, the authors will describe how, when, and why HRMS (specifically Q-Exactive series mass spectrometers) should be considered for implementation in regulated quantitative bioanalysis assays.

Inflammation Thread Runs across Medical Laboratory Specialities

We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding. The C4 component serum levels depend on sufficient vitamin D whilst low vitamin D is inversely related to IgG1, IgA, and C3 linking vitamin sufficiency to innate immunity. Whole genome sequencing of microbial organisms may distinguish virulent from nonvirulent and antibiotic resistant from nonresistant varieties of the same species and thus can be listed in personal big data banks including microbiological pathology; the big data warehouse continues to grow.