Comprehensive lipid analysis of green Arabica coffee beans by LC-HRMS/MS

Lipids play an important role in coffee bean development, coffee brew and in the effects of coffee on human health. They account for around 17% of the dry bean weight and encompass different classes and subclasses, mostly triacylglycerols (TAG) and a minor quantity of phospholipids (PL) and ^βN-alkanoyl-5-hydroxytryptamides (C-5HT). To comprehensive profile these different lipids, it is important to evaluate extraction methods that provide high lipid coverage and to analyze the lipids in high-resolution techniques. In this work, liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) was employed to comprehensive profile lipids from green Arabica coffee beans and to evaluate the extraction efficiency and lipid coverage of three methods: Bligh-Dyer (BD), Folch (FO), and Matyash (MA). The MA method yielded the greatest number of annotated compounds (131 lipids) compared to the other methods. In the positive electrospray ionization (ESI) mode, the main difference among extraction methods was observed for TAG and diacylglycerols, whereas for the negative ESI it was observed differences for phosphatidylinositol (PI), lysophosphatidylinositol and phosphatidic acid (p < 0.05). The analysis of coffees from different maturation stages and/or post-harvest processes were also performed using the MA method. Immature beans were discriminated from mature and overripe beans by its lower levels of C-5HT, PI, phosphatidylcholine, lysophosphatidylcholine, phosphatidylethanolamine, and lysophosphatidylethanolamine. These results can help to better understand the coffee lipid composition and its association with coffee quality.

Analytical Strategies for Fingerprinting of Antioxidants, Nutritional Substances, and Bioactive Compounds in Foodstuffs Based on High Performance Liquid Chromatography-Mass Spectrometry: An Overview

New technology development and globalisation have led to extreme changes in the agri-food sector in recent years that need an important food supply chain characterisation from plant materials to commercial productions. Many analytical strategies are commonly utilised in the agri-food industry, often using complementary technologies with different purposes. Chromatography on-line coupled to mass spectrometry (MS) is one of the most selective and sensitive analytical methodologies. The purpose of this overview is to present the most recent MS-based techniques applied to food analysis. An entire section is dedicated to the recent applications of high-resolution MS. Covered topics include liquid (LC)– and gas chromatography (GC)–MS analysis of natural bioactive substances, including carbohydrates, flavonoids and related compounds, lipids, phenolic compounds, vitamins, and other different molecules in foodstuffs from the perspectives of food composition, food authenticity and food adulteration. The results represent an important contribution to the utilisation of GC–MS and LC–MS in the field of natural bioactive compound identification and quantification.

Competition for growth substrates in river water between Escherichia coli and indigenous bacteria illustrated by high-resolution mass spectrometry

Escherichia coli normally cannot grow in the environment. One environmental stress that prevents E. coli growth may be the competition for growth substrates with co-existing micro-organisms. In this study, the growth substrates of E. coli were screened by high-resolution mass spectrometry and compared with those of indigenous bacteria in river water. In an incubation experiment, E. coli multiplied in sterilized river water, but did not multiply when indigenous micro-organisms were present in the water. By analysing dissolved organic matter in the river water before and after E. coli growth, 35 compounds were identified as putative growth substrates of E. coli. Among them, 33 compounds were also identified as putative growth substrates of indigenous bacteria. These results indicate that E. coli and indigenous bacteria compete for organic substrates in river water, which could suppress the growth of E. coli.

Enhanced protocol for quantitative N-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™

The analysis of N-linked glycans using liquid chromatography and mass spectrometry (LC-MS) presents significant challenges, particularly owing to their hydrophilic nature. To address these difficulties, a variety of derivatization methods have been developed to facilitate improved ionization and detection sensitivity. One such method, the Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™ strategy for labeling glycans, has previously been utilized in the analysis of N- and O-linked glycans in biological samples. To assess the maximum sensitivity and separability of the INLIGHT™ preparation and analysis pipeline, several critical steps were investigated. First, recombinant and nonrecombinant sources of PNGase F were compared to assess variations in the released glycans. Second, modifications in the INLIGHT™ derivatization step were evaluated including temperature optimization, solvent composition changes, reaction condition length and tag concentration. Optimization of the modified method resulted in 20-100 times greater peak areas for the detected N-linked glycans in fetuin and horseradish peroxidase compared with the standard method. Furthermore, the identification of low-abundance glycans, such as (Fuc)1(Gal)2(GlcNAc)4(Man)3(NeuAc)1 and (Gal)3(GlcNAc)5(Man)3(NeuAc)3, was possible. Finally, the optimal LC setup for the INLIGHT™ derivatized N-linked glycan analyses was found to be a C18 reverse-phase (RP) column with mobile phases typical of RPLC.

Lipidomic profiling of single mammalian cells by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)

To better understand cell-to-cell heterogeneity, advanced analytical tools are in a growing demand for elucidating chemical compositions of each cell within a population. However, the progress of single-cell chemical analysis has been restrained by the limitations of small cell volumes and minute cellular concentrations. Here, we present a rapid and sensitive method for investigating the lipid profiles of isolated single cells using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry (IR-MALDESI-MS). In this work, HeLa cells were dispersed onto a glass slide, and the cellular contents were ionized by IR-MALDESI and measured using a Q-Exactive HF-X mass spectrometer. Importantly, this approach does not require extraction and/or enrichment of analytes prior to MS analysis. Using this approach, 45 distinct lipid species, predominantly phospholipids, were detected and putatively annotated from the single HeLa cells. The proof-of-concept study demonstrates the feasibility and efficacy of IR-MALDESI-MS for rapid lipidomic profiling of single cells, which provides an important basis for future work on differentiation between normal and diseased cells at various developmental states, which can offer new insights into cellular metabolic pathways and pathological processes. Although not yet accomplished, we believe this approach can be readily used as an assessment tool to compare the number of identified species during source evolution and method optimization (intra-laboratory), and also disclose the complementary nature of different direct analytical approaches for the coverage of different types of endogenous analytes (inter-laboratory).Graphical abstract.

PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation

The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This is achieved by equally dividing the conventional DIA analysis covering the entire mass range into multiple injections for DIA analyses with complementary windows. Using mouse liver digests, the PulseDIA method identified up to 50% more peptides and 29% more protein groups than that by conventional DIA with the same length of effective gradient time. Compared to conventional multi-injection GPF, PusleDIA exhibited higher flexibility and identified up to 18% more peptides and 8% more protein groups using two injections. The gain of peptides per effective time unit was the highest in PulseDIA compared to conventional DIA and GPF. We further applied the PulseDIA method to profile the proteome of 18 human tissue samples (benign and malignant) from nine cholangiocarcinoma (CCA) patients. PulseDIA identified 7796 protein groups in these CCA samples, with a 14% increase of protein group identification compared to the conventional DIA method. The missing value for protein matrix dropped by 7% using PulseDIA compared to DIA. A total of 681 significantly altered proteins were detected in CCA samples using PulseDIA, including several dysregulated proteins, which were absent in the conventional DIA analysis. Taken together, we present PulseDIA as an enhanced DIA-MS method with improved sensitivity and reproducibility.

An untargeted metabolomics strategy to measure differences in metabolite uptake and excretion by mammalian cell lines

INTRODUCTION

It is widely but erroneously believed that drugs get into cells by passing through the phospholipid bilayer portion of the plasma and other membranes. Much evidence shows, however, that this is not the case, and that drugs cross biomembranes by hitchhiking on transporters for other natural molecules to which these drugs are structurally similar. Untargeted metabolomics can provide a method for determining the differential uptake of such metabolites.

OBJECTIVES

Blood serum contains many thousands of molecules and provides a convenient source of biologically relevant metabolites. Our objective was to detect and identify metabolites present in serum, but to also establish a method capable of measure their uptake and secretion by different cell lines.

METHODS

We develop an untargeted LC-MS/MS method to detect a broad range of compounds present in human serum. We apply this to the analysis of the time course of the uptake and secretion of metabolites in serum by several human cell lines, by analysing changes in the serum that represents the extracellular phase (the 'exometabolome' or metabolic footprint).

RESULTS

Our method measures some 4000-5000 metabolic features in both positive and negative electrospray ionisation modes. We show that the metabolic footprints of different cell lines differ greatly from each other.

CONCLUSION

Our new, 15-min untargeted metabolome method allows for the robust and convenient measurement of differences in the uptake of serum compounds by cell lines following incubation in serum. This will enable future research to study these differences in multiple cell lines that will relate this to transporter expression, thereby advancing our knowledge of transporter substrates, both natural and xenobiotic compounds.

HUMOS: How to Understand My Orbitrap Spectrum?-An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics

The Orbitrap mass analyzer can provide high mass accuracy and throughput, which has significantly improved proteome research and made this type of instrumentation one of the most frequently applied in proteomics. The efficient use of Orbitrap mass spectrometers requires training. Students in the field of proteomics can benefit from a deeper understanding of the Orbitrap technology to comprehend mass spectral interpretation, troubleshooting, and judgment of experimental settings. Unfortunately, the cost of high-end mass spectrometers limits the implementation of this type of equipment in educational laboratories. Guided by these concerns, we developed an eLearning web application called HUMOS aimed to help teach Orbitrap mass spectrometry. Although a typical proteomics experiment includes the use of several different technologies, such as liquid chromatography, mass spectrometry, and bioinformatics, the learning objectives of HUMOS are focused on mass spectrometry. HUMOS models a mass spectrum of a peptide mixture, allowing us to investigate the influence of mass spectral acquisition parameters. By changing the parameters and observing the differences, students can learn more about the mass spectral resolution, duty cycle, throughput of the analysis, ion accumulation, and spectral dynamic range and get familiar with advanced spectral acquisition methods, such as BoxCar. HUMOS is an open-source software published under the Apache license; the live installation is available at http://humos.bmb.sdu.dk.

Rapid characterization of Schisandra species by using direct analysis in real time mass spectrometry

Direct analysis in real time ionization source coupled with quadrupole orbitrap mass spectrometry (DART-Q-Orbitrap MS) was applied to analyze the Schisandra chinensis (S. chinensis) and Schisandra sphenanthera (S. sphenanthera) samples. The experimental condition including the ionization gas and gas temperature were optimized to obtain the best performance. The DART-MS analysis was operated using helium at 250 °C. The partial least squares discriminant analysis (PLS-DA) was conducted based on the DART-MS data to explore the differences between S. chinensis and S. sphenanthera samples. The clear separation between groups was observed in the PLS-DA score plot, indicating the chemome diversity of these two samples. Then 8 compounds that contribute most to the sample classification were selected and annotated, and the intensity change tendency of these compounds was similar to that obtained by the high-performance liquid chromatography (HPLC) method. Besides, these two species can also be discriminated by examining the existence of the compound anwulignan at m/z 328.1656 in this study. Our results show that DART-MS is a powerful analytical tool with the merit of rapid analysis speed, easy to handle, low consumption of organic solvent, and has the great potential for rapid detection and discrimination of S. chinensis and S. sphenanthera. It is expected that the established method could provide a rapid, reliable method for the quality assessment of Schisandra species, and expand this method to the analysis of other herbal medicines.

Comparative Proteomic Analysis of Wild Type and Mutant Lacking an SCF E3 Ligase F-Box Protein in Magnaporthe oryzae

Magnaporthe oryzae (M. oryzae) is a pathogenic, filamentous fungus that is a primary cause of rice blast disease. The M. oryzae protein MGG_13065, SCF E3 ubiquitin ligase complex F-box protein, has been identified as playing a crucial role in the infection process, specifically, as part of the ubiquitin mediated proteolysis pathway. Proteins targeted by MGG_13065 E3 ligase are first phosphorylated and then ubiquitinated by E3 ligase. In this study, we used a label-free quantitative global proteomics technique to probe the role of ubiquitination and phosphorylation in the mechanism of how E3 ligase regulates change in virulence of M. oryzae. To do this, we compared the WT M. oryzae 70-15 strain with a gene knock out (E3 ligase KO) strain. After applying a ≥ 5 normalized spectral count cutoff, a total of 4432 unique proteins were identified comprised of 4360 and 4372 in the WT and E3 ligase KO samples, respectively. Eighty proteins drastically increased in abundance, while 65 proteins decreased in abundance in the E3 ligase KO strain. Proteins (59) were identified only in the WT strain; 13 of these proteins had both phosphorylation and ubiquitination post-translational modifications. Proteins (71) were revealed to be only in the E3 ligase KO strain; 23 of the proteins have both phosphorylation and ubiquitination post-translational modifications. Several of these proteins were associated with key biological processes. These data greatly assist in the selection of future genes for functional studies and enable mechanistic insight related to virulence.

Technical Overview of Orbitrap High Resolution Mass Spectrometry and Its Application to the Detection of Small Molecules in Food (Update Since 2012)

Food safety and quality issues are becoming increasingly important and attract much attention, requiring the development of better analytical platforms. For example, high-resolution (especially Orbitrap) mass spectrometry simultaneously offers versatile functions such as targeted/non-targeted screening while providing qualitative and quantitative information on an almost unlimited number of analytes to facilitate routine analysis and even allows for official surveillance in the food field. This review covers the current state of Orbitrap mass spectrometry (OMS) usage in food analysis based on research reported in 2012-2019, particularly highlighting the technical aspects of OMS application and the achievement of OMS-based screening and quantitative analysis in the food field. The gained insights enhance our understanding of state-of-the-art high-resolution mass spectrometry and highlight the challenges and directions of future research.

Transient-Mediated Simulations of FTMS Isotopic Distributions and Mass Spectra to Guide Experiment Design and Data Analysis

Fourier transform mass spectrometry (FTMS) applications require accurate analysis of extremely complex mixtures of species in wide mass and charge state ranges. To optimize the related FTMS data analysis accuracy, parameters for data acquisition and the allied data processing should be selected rationally, and their influence on the data analysis outcome is to be understood. To facilitate this selection process and to guide the experiment design and data processing workflows, we implemented the underlying algorithms in a software tool with a graphical user interface, FTMS Isotopic Simulator. This tool computes FTMS data via time-domain data (transient) simulations for user-defined molecular species of interest and FTMS instruments, including diverse Orbitrap FTMS models, followed by user-specified FT processing steps. Herein, we describe implementation and benchmarking of this tool for analysis of a wide range of compounds as well as compare simulated and experimentally generated FTMS data. In particular, we discuss the use of this simulation tool for narrowband, broadband, and low- and high-resolution analysis of small molecules, peptides, and proteins, up to the level of their isotopic fine structures. By demonstrating the allied FT processing artifacts, we raise awareness of a proper selection of FT processing parameters for modern applications of FTMS, including intact mass analysis of proteoforms and top-down proteomics. Overall, the described transient-mediated approach to simulate FTMS data has proven useful for supporting contemporary FTMS applications. We also find its utility in fundamental FTMS studies and creating didactic materials for FTMS teaching.

High Levels of Anabaenopeptins Detected in a Cyanobacteria Bloom from N.E. Spanish Sau-Susqueda-El Pasteral Reservoirs System by LC-HRMS

The appearance of a bloom of cyanobacteria in the Sau-Susqueda-El Pasteral system (River Ter, NE Spain) in the autumn of 2015 has been the most recent episode of extensive bloom detected in Catalonia. This system is devoted mainly to urban supply, regulation of the river, irrigation and production of hydroelectric energy. In fact, it is one of the main supply systems for the metropolitan area of cities such as Barcelona and Girona. An assessment and management plan was implemented in order to minimize the risk associated to cyanobacteria. The reservoir was confined and periodic sampling was carried out. Low and high toxicity was detected by cell bioassays with human cell lines. Additionally, analysis studies were performed by enzyme-linked immunosorbent assay (ELISA) and liquid chromatography–high resolution mass spectrometry (LC–HRMS). A microcystin target analysis and suspect screening of microcystins, nodularins, cylindrosperpmopsin and related cyanobacterial peptides by LC–HRMS were applied. The results for the analysis of microcystins were negative (<0.3 μg/L) in all the surface samples. Only traces of microcystin-LR, -RR and -dmRR were detected by LC–HRMS in a few ng/L from both fractions, aqueous and sestonic. In contrast, different anabaenopeptins and oscillamide Y at unusually high concentrations (µg-mg/L) were observed. To our knowledge, no previous studies have detected these bioactive peptides at such high levels. The reliable identification of these cyanobacterial peptides was achieved by HRMS. Although recently these peptides are detected frequently worldwide, these bioactive compounds have received little attention. Therefore, more studies on these substances are recommended, especially on their toxicity, health risk and presence in water resources.

Carotenoid composition and antioxidant potential of Eucheuma denticulatum, Sargassum polycystum and Caulerpa lentillifera

Three species of Malaysian edible seaweed (Eucheuma denticulatum, Sargassum polycystum and Caulerpa lentillifera) were analyzed for their carotenoid composition using a combination of high-performance thin layer chromatography (HPTLC) and ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS), while the antioxidant capacities were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and oxygen radical absorbance capacity (ORAC) assays. The HPTLC analysis exhibited a distinct carotenoid pattern among the three seaweed groups. The UHPLC-ESI-MS/MS analysis showed fucoxanthin as the major carotenoid present in S. polycystum while lutein and zeaxanthin in E. denticulatum. For C. lentillifera, β-carotene and canthaxanthin were the major carotenoids. Some of the carotenoids, such as rubixanthin, dinoxanthin, diatoxanthin and antheraxanthin, were also tentatively detected in E. denticulatum and S. polycystum. For antioxidant activity, S. polycystum (20 %) and E. denticulatum (1128 μmol TE/g) showed the highest activity in the DPPH and ORAC assays, respectively. The findings suggest the three edible varieties of seaweeds may provide a good dietary source with a potential to reduce antioxidative stress.

Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides

Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians’ associated organisms and their products, but proteomic studies are still scarce. Hence, we explored the tunic of three ascidian species using a shotgun proteomics approach. Proteins extracted from the tunic of Ciona sp., Molgula sp., and Microcosmus sp. were processed using a nano LC-MS/MS system (Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer). Raw data was searched against UniProtKB – the Universal Protein Resource Knowledgebase (Bacteria and Metazoa section) using Proteome Discoverer software. The resulting proteins were merged with a non-redundant Antimicrobial Peptides (AMPs) database and analysed with MaxQuant freeware. Overall, 337 metazoan and 106 bacterial proteins were identified being mainly involved in basal metabolism, cytoskeletal and catalytic functions. 37 AMPs were identified, most of them attributed to eukaryotic origin apart from bacteriocins. These results and the presence of “Biosynthesis of antibiotics” as one of the most highlighted pathways revealed the tunic as a very active tissue in terms of bioactive compounds production, giving insights on the interactions between host and associated organisms. Although the present work constitutes an exploratory study, the approach employed revealed high potential for high-throughput characterization and biodiscovery of the ascidians’ tunic and its microbiome.

Fluorine and nitrogen functionalized magnetic graphene as a novel adsorbent for extraction of perfluoroalkyl and polyfluoroalkyl substances from water and functional beverages followed by HPLC-Orbitrap HRMS determination

Most of the reported magnetic adsorbents are difficult to absorb multi-class of per- and polyfluoroalkyl substances (PFASs), especially the short-chain PFASs. In this work, a novel fluorine and nitrogen functionalized magnetic graphene (G-NH-FBC/Fe₂O₃) was first synthesized and characterized by scanning electron microscope (SEM), Fourier Transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) and vibrating sample magnetometer (VSM). The as-prepared G-NH-FBC/Fe₂O₃ was utilized as adsorbents for the magnetic solid-phase extraction (MSPE) of 19 PFASs from water and functional beverages and showed excellent adsorption capacity probably due to the hydrophobic interaction. Under the optimal pretreatment and instrumental conditions, a selective and sensitive high performance liquid chromatography Orbitrap high resolution mass spectrometry (HPLC-Orbitrap HRMS) method was developed for the determination of PFASs. Results indicated that the proposed method had favorable linearity (R² ≥ 0.994) within a wide range of concentrations. Limit of detection (LOD) and limit of quantification (LOQ) for the developed method ranged from 3 ng/L to 15 ng/L and 10 ng/L to 49 ng/L, respectively. Finally, the method was successfully applied to determine PFASs in drinking water, river water, tap water, factory drainage and functional beverages with recoveries ranging from 71.9% to 117.6% and relative standard deviation of <10%. The prepared G-NH-FBC/Fe₂O₃ was easy to recycle and could be reused for five times without significant decrease in extraction recoveries of PFASs. These results demonstrated that this novel magnetic G-NH-FBC/Fe₂O₃ could efficiently enrich PFASs and the proposed method is reliable and robust for the determination of PFASs in water and beverage samples.

Optimization of mass spectrometry settings for steroidomic analysis in young and old killifish

Steroids are essential structural components of cell membranes that organize lipid rafts and modulate membrane fluidity. They can also act as signalling molecules that work through nuclear and G protein–coupled receptors to impact health and disease. Notably, changes in steroid levels have been implicated in metabolic, cardiovascular and neurodegenerative diseases, but how alterations in the steroid pool affect ageing is less well understood. One of the major challenges in steroidomic analysis is the ability to simultaneously detect and distinguish various steroids due to low in vivo concentrations and naturally occurring stereoisomers. Here, we established such a method to study the mass spectrometry behaviour of nine sterols/steroids and related molecules (cholesterol precursors: squalene, lanosterol; sterol metabolites; 7 Dehydrocholesterol, 24, 25 and 27 Hydroxycholesterol; and steroids: progesterone, testosterone, and corticosterone) during ageing in the African turquoise killifish, a new model for studying vertebrate longevity. We find that levels of all tested steroids change significantly with age in multiple tissues, suggesting that specific steroids could be used as biomarkers of ageing. These findings pave the way for use of Nothobranchius furzeri as a novel model organism to unravel the role of sterols/steroids in ageing and age-related diseases.

Molecular characterization of water extractable Euglena gracilis cellular material composition using asymmetrical flow field-flow fractionation and high-resolution mass spectrometry

Asymmetrical flow field-flow fractionation (AF4) and high-resolution Orbitrap mass spectrometry (HRMS) were used to separate and characterize cellular fractions of the dark- and light-grown Euglena gracilis cellular material. Biological replicates analyzed by HRMS shared 21-73% of commonly detected m/z values. Greater variability in shared features was found in light-grown cellular fractions (p < 0.05), likely due to small variations in growth stage. Significant differences in molecular composition were observed between AF4 cellular fractions, with dark cell fractions showing a propensity towards carbohydrate-like and tannin-like compounds, and higher double-bond equivalent (DBE) and modified aromatic index (AI_mod) were associated with light-grown cell fractions. Fractionation and high-resolution mass spectrometry aided characterization demonstrated the power of the AF4 to selectively cater to certain compounds/cellular entities with distinct compositional classes and double-bond equivalents and aromaticity index characteristics. Graphical abstract.

Assessing accuracy, precision and selectivity using quality controls for non-targeted analysis

The benchmarks to assess reproducibility are not well defined for non-target analysis. Parameters to evaluate analytical performance, such as accuracy, precision and selectivity, are well defined for target analysis, but remain elusive for non-target screening analysis. In this study, quality control (QC) guidelines are proposed to assure reliable data in non-target screening methodologies using a simple set of standards. Workflow reproducibility was assessed using an in-house QC mixture containing selected compounds with a wide range of polarity that can be detected either by electrospray ionization (ESI) in positive or negative mode. The analysis was performed by online solid phase extraction (SPE) liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS). Data processing was done by a commercially available software, Compound Discoverer v. 3.0 using an environmental working template, which searched a multitude of databases, including Chemspider, EPA Toxcast, MzCloud among others. We have specifically evaluated method specificity, precision, accuracy and reproducibility in terms of peak area and retention time variability, true positive identification rate, intraday (within days) and interday (consecutive days) variations and the use of QC samples to reduce false positives. The method showed a satisfactory accuracy with an identification rate of ≥70% for most of the QC compounds. Precision estimated based on peak area relative standard deviation (RSD) ranged between 30 and 50% for most of the compounds. Data normalization to a single internal standard did not improve peak area variability. Retention time precision showed great repeatability and reproducibility (RSD ≤ 5%). In addition, a simple model of RT vs log K_ow was designed based on our QC mixtures to efficiently reduced false positives by an average of 49.1%.

MS2 and LC libraries for untargeted metabolomics: Enhancing method development and identification confidence

As part of the "omics" technologies in the life sciences, metabolomics is becoming increasingly important. In untargeted metabolomics, unambiguous metabolite identification and the inevitable coverage bias that comes with the selection of analytical conditions present major challenges. Reliable compound annotation is essential for translating metabolomics data into meaningful biological information. Here, we developed a fast and transferable method for generating in-house MS² libraries to improve metabolite identification. Using the new method we established an in-house MS² library that includes over 4,000 fragmentation spectra of 506 standard compounds for 6 different normalized collision energies (NCEs). Additionally, we generated a comprehensive liquid chromatography (LC) library by testing 57 different LC-MS conditions for 294 compounds. We used the library information to develop an untargeted metabolomics screen with maximum coverage of the metabolome that was successfully tested in a study of 360 human serum samples. The current work demonstrates a workflow for LC-MS/MS-based metabolomics, with enhanced metabolite identification confidence and the possibility to select suitable analysis conditions according to the specific research interest.

Vaccinium macrocarpon (Cranberry)-Based Dietary Supplements: Variation in Mass Uniformity, Proanthocyanidin Dosage and Anthocyanin Profile Demonstrates Quality Control Standard Needed

Vaccinium macrocarpon (syn. American Cranberry) is employed in dietary supplements (DS) with the aim to improve urinary tract well-being. This property is linked to the antiadhesion-activity of proanthocyanidins (PACs) against uropathogenic-bacteria. However, the current European legislation has been criticized for being weak and ineffective. Indeed, recent scientific works report mislabeled, contaminated, and adulterated supplements containing dangerous or unknown compounds, or sold at toxic doses. In this work, we analysed 24 DS that claim to contain cranberry, and to have a specific dosage of PACs. Our tests included the control of the good manufacturing practice according to the European Pharmacopoeia, and the verification of the claimed dosage of PACs. Moreover, in order to confirm the real presence of cranberry in DS, chemical fingerprinting via HPLC-UV/Vis-MS/MS was employed. Our results showed that 17 DS did not comply with the uniformity test of dosage forms, and only five contained cranberry. Finally, 16 DS claimed an incorrect amount of PACs. These data suggest that several cranberry-based DS are present in the European market with insufficient quality controls. Considering that often DS are self-prescribed by consumer relying on their claim, the data obtained in this work should encourage more controls and stricter rules.

Two-dimensional hydrophilic interaction and reversed phase liquid chromatography easily extracted pesticides and polar pesticides multi-residue method--A concept

We offer a concept for the simultaneous determination of QuEChERS amenable and highly polar pesticides using two-dimensional liquid chromatography high resolution mass spectrometry with electrospray ionization (ESI) and polarity switching. First results proved feasibility to determine glyphosate, AMPA, ethephon, glufosinate, MPPA, fosetyl-Al, N-acetyl-glufosinate, N-acetyl-glyphosate and N-acetyl-AMPA including fragments, next to 325 QuEChERS amenable pesticides. We plan to investigate an efficient extraction procedure by either diluting with water or acetonitrile extraction in mini scale without the need for additional clean-up steps. After completion of all experiments, the method will be validated and expanded for further pesticides and organic contaminants. Therefore, we present a concept for a Two-dimensional HILIC Reversed phase Easily Extracted Pesticides and Polar Pesticides (THREEP or ₃P⁽⁺⁾) multi-residue method.

New Energy Setup Strategy for Intact N-Glycopeptides Characterization Using Higher-Energy Collisional Dissociation

With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptides characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30 ± 10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of an independent NCEs setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR ≤ 1%, site-specific IDs with site-determining fragment ions, and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767 → 6,746), 57% (599 → 942), and 97% (1771 → 3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.

Development of an integral strategy for non-target and target analysis of site-specific potential contaminants in surface water: A case study of Dianshan Lake, China

Surface water contains a large number of potential pollutants and their transformation products, which cannot be discovered by normal target analysis alone. To detect site-specific and unknown contaminants in the environment, we established an integral analytical strategy based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) combined with data processing using specific software (Compound Discoverer 3.0). In this case study of Dianshan Lake, 95 potential contaminants were tentatively identified and ranked by the scoring system. Then, the 95 compounds were categorized into 4 subgroups: pesticides, drugs, plastic additives and surfactants. To determine the sources and distribution of those pollutants, 4 heat maps were developed based on the sum of peak areas of respective categories. In addition, 19 substances with high exposure risk among the 95 compounds tentatively identified were confirmed and quantified. In the present study, the analytical strategy with non-target screening followed by target analysis demonstrated that pesticides and plastic additives are the two dominant types of contaminants in Dianshan Lake. High accuracy and high-resolution data combined with integrated software provided abundant information for the identification of a wide range of potential contaminants in the environment. This approach can be a useful tool for the simple and rapid screening and tentative detection of site-specific contaminants.