Metabolomics 2022 workshop report: state of QA/QC best practices in LC-MS-based untargeted metabolomics, informed through mQACC community engagement initiatives.

INTRODUCTION: The Metabolomics Quality Assurance and Quality Control Consortium (mQACC) organized a workshop during the Metabolomics 2022 conference. OBJECTIVES: The goal of the workshop was to disseminate recent findings from mQACC community-engagement efforts and to solicit feedback about a living guidance document of QA/QC best practices for untargeted LC-MS metabolomics. METHODS: Four QC-related topics were presented. RESULTS: During the discussion, participants expressed the need for detailed guidance on a broad range of QA/QC-related topics accompanied by use-cases. CONCLUSIONS: Ongoing efforts will continue to identify, catalog, harmonize, and disseminate QA/QC best practices, including outreach activities, to establish and continually update QA/QC guidelines.

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria.

Metabarcoding is a powerful tool to characterize biodiversity in biological samples. The interpretation of taxonomic profiles from metabarcoding data has been hindered by their compositional nature. Several strategies have been proposed to transform compositional data into quantitative data, but they have intrinsic limitations. Here, I propose a workflow based on bacterial and fungal cellular internal standards (spike-ins) for absolute quantification of the microbiota in soil samples. These standards were added to the samples before DNA extraction in amounts estimated after qPCRs, to target around 1-2% coverage in the sequencing run. In bacteria, proportions of spike-in reads in the sequencing run were very similar (< 2-fold change) to those predicted by the qPCR assessment, and for fungi they differed up to 40-fold. The low variation among replicates highlights the reproducibility of the method. Estimates based on multiple bacterial spike-ins were highly correlated (r = 0.99). Procrustes analysis evidenced significant biological effects on the community composition when normalizing compositional data. A protocol based on qPCR estimation of input amounts of cellular spikes is proposed as a cheap and reliable strategy for quantitative metabarcoding of biological samples.

Amino acid analysis for peptide quantitation using reversed-phase liquid chromatography combined with multiple reaction monitoring mass spectrometry.

Amino acid analysis (AAA) can be used for absolute quantitation of standard peptides after acid hydrolysis using 6 M HCl. Obtained individual amino acids can then be quantified by liquid chromatography-mass spectrometry (LC-MS). Achieving baseline separation of non-derivatized amino acids is challenging when reversed-phase (RP) chromatography is used. Several derivatization methods are commonly utilized to address this issue; however, derivatization has several drawbacks, such as derivative instability and lack of reproducibility. Currently, separation of non-derivatized amino acids is typically done using HILIC, but HILIC has problems of poor reproducibility and long column equilibration times. We developed a method to quantify non-derivatized amino acids, including methionine and cysteine, from peptide hydrolysates by RP-LC-MS without special pre-treatment of the samples. Samples were spiked with certified isotopically labeled (13C- and/or 15N-) amino acids as internal standards. The amino acids released from acid hydrolysis were then analyzed by RP-UPLC-MRM-MS and quantified using the analyte/internal standard chromatographic peak area ratios. Peptide quantitation was based on the sum of the individual amino acid concentrations from the known peptide sequences. The resulting method did not require derivatization, used standard C18-based reversed-phase liquid chromatography, did not require external calibration, was robust, and was able to quantify all 17 amino acids for which we had internal standards, including the sulfur-containing amino acids, cysteine and methionine, in their respective oxidized forms. This simple and robust method enabled the absolute quantitation of standard peptides using only acid hydrolysis and a standard RP-UPLC-MRM-MS setup.

STRATEGIES AND CHALLENGES IN METHOD DEVELOPMENT AND VALIDATION FOR THE ABSOLUTE QUANTIFICATION OF ENDOGENOUS BIOMARKER METABOLITES USING LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY.

Metabolomics is a dynamically evolving field, with a major application in identifying biomarkers for drug development and personalized medicine. Numerous metabolomic studies have identified endogenous metabolites that, in principle, are eligible for translation to clinical practice. However, few metabolomic-derived biomarker candidates have been qualified by regulatory bodies for clinical applications. Such interruption in the biomarker qualification process can be largely attributed to various reasons including inappropriate study design and inadequate data to support the clinical utility of the biomarkers. In addition, the lack of robust assays for the routine quantification of candidate biomarkers has been suggested as a potential bottleneck in the biomarker qualification process. In fact, the nature of the endogenous metabolites precludes the application of the current validation guidelines for bioanalytical methods. As a result, there have been individual efforts in modifying existing guidelines and/or developing alternative approaches to facilitate method validation. In this review, three main challenges for method development and validation for endogenous metabolites are discussed, namely matrix effects evaluation, alternative analyte-free matrices, and the choice of internal standards (ISs). Some studies have modified the equations described by the European Medicines Agency for the evaluation of matrix effects. However, alternative strategies were also described; for instance, calibration curves can be generated in solvents and in biological samples and the slopes can be compared through ratios, relative standard deviation, or a modified Stufour suggested approaches while quantifying mainly endogenous metabolitesdent t-test. ISs, on the contrary, are diverse; in which seven different possible types, used in metabolomics-based studies, were identified in the literature. Each type has its advantages and limitations; however, isotope-labeled ISs and ISs created through isotope derivatization show superior performance. Finally, alternative matrices have been described and tested during method development and validation for the quantification of endogenous entities. These alternatives are discussed in detail, highlighting their advantages and shortcomings. The goal of this review is to compare, apprise, and debate current knowledge and practices in order to aid researchers and clinical scientists in developing robust assays needed during the qualification process of candidate metabolite biomarkers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC).

INTRODUCTION: The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES: This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS: The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS: The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.

Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics.

In mass spectrometry-based proteomics, heavy internal standards are used to validate target peptide detections and to calibrate peptide quantitation. Here, we report light contamination present in heavy labelled synthetic peptides of high isotopic enrichment. Application of such peptides as assay-internal standards potentially compromises the detection and quantitation especially of low abundant cellular peptides. Therefore, it is important to adopt guidelines to prevent false-positive identifications of endogenous light peptides as well as errors in their quantitation from biological samples.

Development of LC-MS-ESI-TOF method for quantification of phytates in food using 13C-labelled maize as internal standard.

In this work, the LC-MS-ESI-TOF method for simultaneous determination of phytates (inositol mono-, bis-, tris-, tetrakis-, pentakis-, and hexakisphosphates, abbreviated to IP1, IP2, IP3, IP4, IP5, and IP6, respectively) in food samples was developed and validated. The suitability of U-13C-labelled maize as a source for labelled internal standards for quantification of phytates was elucidated. The effectiveness of liberating IP1, IP2, IP3, IP4, and IP5 from phytic acid extracted form U-13C-labelled maize was evaluated for a variety of hydrolysis conditions, including enzymatic and acid hydrolysis. Enzymatic degradation of phytic acid using phytase (PHYZYME XP 5000 L) was very effective; phytic acid was degraded to lower phytates, but their distribution was unequal. Chemical hydrolysis was conducted under acidic conditions using hydrochloric acid and elevated temperatures up to 140 °C. The highest yields of IP4, IP5, and IP6 and of IP1, IP2, and IP3 were achieved by chemical hydrolysis at 105 °C for 7 h and 24 h, respectively. Thus, a combination of these two chemical treatments was selected for internal standard production. The developed LC-MS-ESI-TOF method was tested and successfully validated using plant-based food samples with different distribution of phytates. With this method, different forms of phytates in foods were separated and quantified simultaneously within 20 min. The high accuracy and precision of the developed method were guaranteed using respective labelled internal standards derived from U-13C-labelled maize.

Performance Assessment of a 125 Human Plasma Peptide Mixture Stored at Room Temperature for Multiple Reaction Monitoring-Mass Spectrometry.

Synthetic peptides are a critical requirement for the development and application of targeted mass spectrometry (MS)-based assays for the quantitation of proteins from biological matrices. Transporting synthetic peptides on dry ice from one laboratory to another is costly and often difficult because of country-specific import and export regulations. Therefore, in this study, we assessed the impact of leaving a lyophilized mixture consisting of 125 peptides at room temperature for up to 20 days, and we assessed the effect on the quantitative performance of multiple reaction monitoring-MS (MRM-MS) assays. The findings suggest that there are no significant differences in the MRM-MS results for the time points assessed in this study (up to 20 days). All the calibration curves and quality control (QC) samples met the acceptance criteria for precision and accuracy (raw data are available via the public MS data repository PanoramaWeb, identifier: /MRM Proteomics/2020_BAK125_RT). The number of endogenous proteins quantifiable across five plasma samples was consistently between 87 and 99 out of 125 for all time points. Moreover, the coefficients of variation (CVs) calculated for the majority of peptide concentrations across all samples and time points were <5%. In addition, a lyophilized peptide mixture was transported from Canada to Iceland without dry ice. The results showed that there was no significant difference in the quantitative performance, with the determined concentrations of most proteins in the samples falling within 30% between the analyses performed on the same three plasma samples in Iceland and those in Canada. Overall, a comparison of the results obtained in Canada and in Iceland indicated that the peptides were stable under the conditions tested and also indicated that shipping lyophilized peptide mixtures without dry ice, but in the presence of sufficient desiccant material, could be a feasible option in cases where transport difficulties may arise or dry-ice sublimation may occur.

Synthesis of 13 C-labelled cutin and suberin monomeric dicarboxylic acids of the general formula HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28).

13 C-labeled dicarboxylic acids HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28) have been synthesized as internal standards for LC-MS and GC-MS analysis of cutin and suberin monomer degradation by soil-based microorganisms. Different synthetic strategies had to be applied depending on the chain length of the respective synthetic target and because of economic considerations. 13 C-labels were introduced by nucleophilic substitution of a suitable leaving group with labelled potassium cyanide and subsequent hydrolysis of the nitriles to produce the corresponding dicarboxylic acids. All new compounds are characterized by GC/MS, IR, and NMR methods as well as by elemental analysis.

Palladium Nanoparticles for the Deuteration and Tritiation of Benzylic Positions on Complex Molecules.

Palladium nanoparticles (PdNp) were revealed as an efficient hydrogen isotope exchange catalyst for the deuterium and tritium labeling of benzylic positions of complex molecules. A practical way to obtain small palladium nanoparticles and to apply them as a catalyst for hydrogen isotope exchange (HIE) is presented. Several model compounds and popular bioactive molecules were submitted to HIE reactions catalyzed by the PdNp. Benzylic positions situated far away from heteroatoms were labeled with high isotopic enrichments. The observed non-directed HIE gave rise to regioselectivities complementary to those obtained with other methods, which typically require specific directing groups. For this reason, the successful deuteration of a broad variety of benzylic positions created a helpful tool to produce internal LC-MS standards of complex drugs. Furthermore, this nanocatalyst paved the way for the radiolabeling of drug molecules with high specific activities by using low pressures of tritium gas.

Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards.

Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies.IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.

Evaluation of pyraoxystrobin bioconcentration in zebrafish (Danio rerio) using modified QuEChERS extraction.

Pyraoxystrobin is a novel strobilurin fungicide that is widely used on many crops. The high log Kow of pyraoxystrobin implies that it tends to accumulate in aquatic organisms. This study optimized the sorbents of QuEChERS (quick, easy, cheap, effective, rugged, and safe) using 13C-labelled pyraoxystrobin as the internal standard (IS). It has been established a QuEChERS-LC-MS/MS IS method to study the bioconcentration and elimination of pyraoxystrobin in zebrafish (Danio rerio). The results indicated that the method had satisfactory linearity between 0.234 and 15 µg L-1 (R2 = 0.9996). The limits of detection (LOD) and quantification (LOQ) for pyraoxystrobin were 0.01 and 0.03 µg L-1, respectively. The LOQs of the method for water and zebrafish were 0.05 µg L-1 and 0.01 mg/kg, respectively. The mean recovery of pyraoxystrobin in zebrafish and water at fortification levels of 0.01-0.3 mg kg-1 and 0.05-1.5 µg L-1 ranged from 98.31 to 105.61% and 101.87 to 108.48%, respectively, with a % RSD (relative standard deviation) of 0.94-3.57%. The bioconcentration has been evaluated. The bioconcentration factors for pyraoxystrobin in zebrafish were 1,792 and 3,505 after exposure to 0.5 µg L-1 for 168 h and 0.05 µg L-1 for 216 h, respectively. The half-life of pyraoxystrobin in zebrafish was 9.0-9.5 d.

Origins of the method of standard additions and of the use of an internal standard in quantitative instrumental chemical analyses.

The origin of the method of standard additions (SAM) and of the use of internal standard (IS) in instrumental chemical analysis and their spread into other areas has been reviewed. Recorded applications of IS range from flame spectroscopy in 1877 through multiple techniques to current use in NMR and standard additions with isotopically labelled internal standards in hyphenated techniques. For SAM, applications stemmed from polarography in 1937 and spread to most instrumental methods. Some misconceptions on priorities are corrected.

Quantification of organic contaminants in urban stormwater by isotope dilution and liquid chromatography-tandem mass spectrometry.

Pollutants transported in urban stormwater runoff induce pervasive water quality degradation in receiving waters. To accurately characterize stormwater quality and treatment system performance across the range of possible contaminant characteristics, comprehensive multi-residue analytical methods are necessary. Here, we developed a solid-phase extraction (SPE) and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method to quantify representative stormwater-derived organic contaminants across multiple chemical classes, including vehicle-related chemicals, corrosion inhibitors, industrial chemicals, pesticides, pharmaceuticals and personal care products, and antioxidants. Extraction conditions, isotope-labeled internal standards, and LC-MS/MS parameters were optimized to enhance recovery, minimize matrix effects, and maximize selectivity and sensitivity. The developed method was sensitive (method quantification limits < 10 ng/L for > 80% of selected analytes) and accurate (mean relative recoveries in the range of 70-130%, with relative standard deviations < 25% for 77% of the analytes) for most of the analytes. The method was used to analyze samples collected from nine urban watersheds during a storm event; 62% of the 39 analytes were detected at least once at concentrations up to 540 ng/L (1,3-diphenylguanidine). Spatial trends in detection and concentration were observed for vehicle-related and industrial chemicals that correlated with vehicle traffic. Total concentrations of pesticides suggested that residential uses could be more important sources than agriculture. This study illustrates the pervasive occurrence of a wide variety of stormwater-derived chemicals in urban receiving waters and highlights the need to better understand their environmental fate and ecological implications. Graphical abstract.

Lipidomics biomarker studies: Errors, limitations, and the future.

Lipidomics is an ever-expanding subfield of metabolomics that surveys 3000 to 5000 individual lipids across more than 56 lipid subclasses, including lipid peroxidation products. Unfortunately, there exists a large number of publications with poor quality data obtained with unit mass resolution leading to many lipid misidentifications. This is further complicated by poor scientific oversight with regard to recognition of isobar issues, sample collection, and sample storage issues that inexplicably requires more detailed attention. Inadvertent or intentional obfuscation of relative quantification data represented as absolute quantification is a subtle but profound difference that may readers outside of the field may not realize, therefore, instigating disservice and unnecessary distrust in the scientific community. These issues need to be addressed aggressively as high quality data are essential for the translation of biomarker research to clinical practice.

Use of phenyl/tetrazolyl-functionalized magnetic microspheres and stable isotope labeled internal standards for significant reduction of matrix effect in determination of nine fluoroquinolones by liquid chromatography-quadrupole linear ion trap mass spectrometry.

In this study, the strategy of unique adsorbent combined with isotope labeled internal standards was used to significantly reduce the matrix effect for the enrichment and analysis of nine fluoroquinolones in a complex sample by liquid chromatography coupled to quadrupole linear ion trap mass spectrometry (LC-QqQLIT-MS/MS). The adsorbent was prepared conveniently by functionalizing Fe3O4@SiO2 microspheres with phenyl and tetrazolyl groups, which could adsorb fluoroquinolones selectively via hydrophobic, electrostatic, and π-π interactions. The established magnetic solid-phase extraction (MSPE) method as well as using stable isotope labeled internal standards in the next MS/MS detection was able to reduce the matrix effect significantly. In the process of LC-QqQLIT-MS/MS analysis, the precursor and product ions of the analytes were monitored quantitatively and qualitatively on a QTrap system equipped simultaneously with the multiple reaction monitoring (MRM) and enhanced product ion (EPI) scan. Subsequently, the enrichment method combined with LC-QqQLIT-MS/MS demonstrated good analytical features in terms of linearity (7.5-100.0 ng mL-1, r > 0.9960), satisfactory recoveries (88.6%-118.3%) with RSDs < 12.0%, LODs = 0.5 µg kg-1 and LOQs = 1.5 µg kg-1 for all tested analytes. Finally, the developed MSPE-LC-QqQLIT-MS/MS method had been successfully applied to real pork samples for food-safety risk monitoring in Ningxia Province, China. Graphical abstract Mechanism of reducing matrix effect through the as-prepared adsorbent.

Quantitative analysis of finasteride tablets dissolution content with non-isotopically labeled internal standard by paper spray ionization mass spectrometry.

Paper spray ionization, one of the ambient mass spectrometry technologies, has been developed to characterize the content of drugs in various complex matrixes including urine, whole blood, dissolution solutions, and so on. An isotopically labeled compound as internal standard is often used in quantitative paper spray ionization experiments. But high cost and difficult to access impede the application of this type of internal standards. Application of non-isotopically labeled compounds as internal standards will make this technology more prevalent. In this paper, we explored the application of finasteride impurity as the internal standard in paper spray ionization-mass spectrometry to measure the dissolution content of finasteride tablets. The new method was optimized and the results were compared to those from high-performance liquid chromatography. The whole analysis time was several minutes and limit of detection for finasteride was around 4.8 ng/mL. The results from paper spray ionization-mass spectrometry were similar to those from high-performance liquid chromatography. Combination of paper spray ionization-mass spectrometry and non-isotopically labeled internal standard renders a new method to analyze drug dissolution content with high specificity, low limit of detection, and simple sample preparation within short time period.

Analysis of retinol, α-tocopherol, 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 in plasma of patients with cardiovascular disease by HPLC-MS/MS method.

Fat-soluble vitamins play a pivotal role in the progression of atherosclerosis and the development of cardiovascular disease. Therefore, plasma monitoring of their concentrations may be useful in the diagnosis of these disorders as well as in the process of treatment. The study aimed to develop and validate an HPLC-MS/MS method for determination of retinol, α-tocopherol, 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 in plasma of patients with cardiovascular disease. The analytes were separated on an HPLC Kinetex F5 column via gradient elution with water and methanol, both containing 0.1% (v/v) formic acid. Detection of the analytes was performed on a triple-quadrupole MS with multiple reaction monitoring via electrospray ionization. The analytes were isolated from plasma samples with liquid-liquid extraction using hexane. Linearity of the analyte calibration curves was confirmed in the ranges 0.02-2 µg/mL for retinol, 0.5-20 µg/mL for α-tocopherol, 5-100 ng/mL for 25-hydroxyvitamin D2 and 2-100 ng/mL for 25-hydroxyvitamin D3. Intra- and inter-assay precision and accuracy of the method were satisfactory. Short- and long-term stabilities of the analytes were determined. The HPLC-MS/MS method was applied for the determination of the above fat-soluble vitamin concentrations in patient plasma as potential markers of the cardiovascular disease progression.

Synthesis of obeticholic acid, a farnesoid X receptor agonist, and its major metabolites labeled with deuterium.

Simple and facile methods for the synthesis of deuterium-labeled obeticholic acid and its 2 metabolites, glycine and taurine conjugates of obeticholic acid, are described herein. The 3 deuterated compounds were applicable for use as internal standards in drug development.

HS-SPME-GC-MS Analyses of Volatiles in Plant Populations-Quantitating Compound × Individual Matrix Effects.

Headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography⁻mass spectrometry (GC-MS) is widely employed for volatile analyses of plants, including mapping populations used in plant breeding research. Studies often employ a single internal surrogate standard, even when multiple analytes are measured, with the assumption that any relative changes in matrix effects among individuals would be similar for all compounds, i.e., matrix effects do not show Compound × Individual interactions. We tested this assumption using individuals from two plant populations: an interspecific grape (Vitis spp.) mapping population (n = 140) and a tomato (Solanum spp.) recombinant inbred line (RIL) population (n = 148). Individual plants from the two populations were spiked with a cocktail of internal standards (n = 6, 9, respectively) prior to HS-SPME-GC-MS. Variation in the relative responses of internal standards indicated that Compound × Individual interactions exist but were different between the two populations. For the grape population, relative responses among pairs of internal standards varied considerably among individuals, with a maximum of 249% relative standard deviation (RSD) for the pair of [U13C]hexanal and [U13C]hexanol. However, in the tomato population, relative responses of internal standard pairs varied much less, with pairwise RSDs ranging from 8% to 56%. The approach described in this paper could be used to evaluate the suitability of using surrogate standards for HS-SPME-GC-MS studies in other plant populations.