bims-metlip 2024-07-07 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2024–07–07
25 papers selected by
Sofia Costa, Matterworks

A practical approach to supported liquid extraction and measurement of 18 steroids in plasma and serum by targeted liquid chromatography tandem mass spectrometry.
Challenges and recent advances in quantitative mass spectrometry-based metabolomics.
Development and evaluation of a candidate reference measurement procedure for detecting 17α-hydroxyprogesterone in dried blood spots using isotope dilution liquid chromatography tandem mass spectrometry.
Broad-spectrum and sensitive screening of more than 1000 compounds in equine urine using liquid chromatography/high-resolution mass spectrometry.
Efficient Strategy for Characterization and Quantification of Polyunsaturated Lipids by Microwave-Assisted MMPP Epoxidation.
Ammonium bicarbonate buffers combined with hybrid surface technology columns improve the peak shape of strongly tailing lipids.
Quantification of treprostinil concentration in rat and human using a novel validated and rapid liquid chromatography-tandem mass spectrometry method: Experimental and clinical applications in ischemia-reperfusion injury.
Bioanalytical validation and clinical application of a liquid chromatography-tandem mass spectrometry method for the quantification of 3-orthomethyldopa, 5-hydroxytryptophan, 5-hydroxyindolacetic acid and homovanillic acid in human cerebrospinal fluid.
Predicting Collision Cross-Section Values for Small Molecules through Chemical Class-Based Multimodal Graph Attention Network.
PANAMA-enabled high-sensitivity dual nanoflow LC-MS metabolomics and proteomics analysis.
[Research progress of deep learning applications in mass spectrometry imaging data analysis].
A rapid LC-MS/MS method for the simultaneous quantification of ivacaftor, lumacaftor, elexacaftor, tezacaftor, hexyl-methyl ivacaftor and ivacaftor carboxylate in human plasma.
Advances in targeted liquid chromatography-tandem mass spectrometry methods for endocannabinoid and N-acylethanolamine quantification in biological matrices: A systematic review.
[Applications of chromatography in glycomics].
Measurement of atmospheric amines and aminoamides by column adsorption/extraction and hydrophilic liquid chromatography-electrospray-tandem mass spectrometry.
Development of a robust non-targeted analysis approach for fast identification of endocrine disruptors and their metabolites in human urine for exposure assessment.
Characterizing lipid constituents of B. moojeni snake venom: a comparative approach for chemical and biological investigations.
Study on the correlation and difference of qualitative information among three types of UPLC-HRMS and potential generalization in metabolites annotation.
Investigating the etiology of Haff disease: Optimization and validation of a sensitive LC-MS/MS method for palytoxins analysis in directly associated freshwater and marine food samples from Brazil.
Probe oscillation control in tapping-mode scanning probe electrospray ionization for stabilization of mass spectrometry imaging.
Evaluation and clinical application of a bracketing calibration-based isotope dilution liquid chromatography-tandem mass spectrometry candidate reference measurement procedure for serum theophylline.
Improved method for quantification of intact oxaliplatin by ultra high performance liquid chromatography-inductively coupled plasma mass spectrometry: Applications to clinical and speciation studies.
Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data.
uafR: An R package that automates mass spectrometry data processing.
Targeted and untargeted metabolomics and lipidomics in dried blood microsampling: Recent applications and perspectives.

MethodsX. 2024 Jun;12 102728

A practical approach to supported liquid extraction and measurement of 18 steroids in plasma and serum by targeted liquid chromatography tandem mass spectrometry.

Scott G Denham, Joanna P Simpson, Federico Diez, Patricia Lee, Catriona Kyle, Ruth Morgan, Natalie Zm Homer.

  Chromatography combined with mass spectrometry is a gold standard technique for steroid measurement, however the type of sample preparation, the dynamic range and reliability of the calibration curve, the chromatographic separation and mass spectrometry settings ultimately determine the success of the method. The steroid biosynthetic pathway is conserved in higher mammals and literature demonstrates that the concentration ranges of different steroid groups are relatively comparable across species. We sought to develop a robust and reliable multi steroid targeted analysis method for blood that would have wide application across higher mammals. The method was developed following bioanalytical method validation guidelines to standards typically applied to human clinical studies, including isotopically labelled internal standards where at all possible. Here we describe the practical approach to a 96-well supported liquid extraction (SLE) method of extraction from plasma (200 µL) using an Extrahera liquid handling robot (Biotage, Sweden), including quality control samples, followed by a comprehensive separation and targeted LC-MS/MS analysis of 18 steroids in plasma (pregnenolone, progesterone, 17α-hydroxyprogesterone, 11-deoxycorticosterone, corticosterone, 11-dehydrocorticosterone, aldosterone, 11-deoxycortisol, 21-deoxycortisol, cortisol, cortisone, androstenedione, testosterone, 5α-dihydrotestosterone, dehydroepiandrosterone, estrone, 17β-estradiol and estriol). •SLE in a 96-well format of up to 74 biological plasma samples, enriched with multiple isotopically labelled internal standards, a 12-point aqueous calibration curve, and 6 serum quality controls, designed to monitor long-term performance of the method•Chromatographic separation of multiple steroids along the gradient, with ammonium fluoride mobile phase additive to improve sensitivity, followed by electrospray ionisation and constant polarity switching•Aqueous calibration standards that cover physiologically relevant ranges - high nanomolar glucocorticoids, low nanomolar androgens and picomolar ranges for estrogens and steroid intermediates.

Keywords:  Automation; Chromatography; Comparative endocrinology; Mass spectrometry; Steroid profiling; Supported liquid extraction and LC-MS/MS analysis of multiple steroids in 200 µL plasma; Targeted

DOI:  https://doi.org/10.1016/j.mex.2024.102728
Anal Sci Adv. 2024 Jun;5(5-6): e2400007

Challenges and recent advances in quantitative mass spectrometry-based metabolomics.

Nathan Ghafari, Lekha Sleno.

  The field of metabolomics has gained tremendous interest in recent years. Whether the goal is to discover biomarkers related to certain pathologies or to better understand the impact of a drug or contaminant, numerous studies have demonstrated how crucial it is to understand variations in metabolism. Detailed knowledge of metabolic variabilities can lead to more effective treatments, as well as faster or less invasive diagnostics. Exploratory approaches are often employed in metabolomics, using relative quantitation to look at perturbations between groups of samples. Most metabolomics studies have been based on metabolite profiling using relative quantitation, with very few studies using an approach for absolute quantitation. Using accurate quantitation facilitates the comparison between different studies, as well as enabling longitudinal studies. In this review, we discuss the most widely used techniques for quantitative metabolomics using mass spectrometry (MS). Various aspects will be addressed, such as the use of external and/or internal standards, derivatization techniques, in vivo isotopic labelling, or quantitative MS imaging. The principles, as well as the associated limitations and challenges, will be described for each approach.

Keywords:  internal standards; mass spectrometry; quantitative metabolomics; stable isotope labelling

DOI:  https://doi.org/10.1002/ansa.202400007
Anal Bioanal Chem. 2024 Jun 29.

Development and evaluation of a candidate reference measurement procedure for detecting 17α-hydroxyprogesterone in dried blood spots using isotope dilution liquid chromatography tandem mass spectrometry.

Ziyun He, Haibing Dai, Jian Shen, Yanjie Huang, Jinsong Liu, Renqing Yan, Feng Zhang, Shengkai Yan.

  17α-Hydroxyprogesterone (17α-OHP) quantification in dried blood spots (DBS) is essential for newborn screening for congenital adrenal hyperplasia (CAH), which is challenging due to its low physiological concentration. The high false-positive rates of immunoassays necessitate the development of more accurate methods. Liquid chromatography tandem mass spectrometry (LC-MS/MS) offers increased specificity and sensitivity, yet standardized procedures for 17α-OHP measurement are required for clinical application. A candidate reference measurement procedure (cRMP) using isotope dilution LC-MS/MS was developed for 17α-OHP quantification in DBS. By utilizing stable isotope-labeled D8-17α-OHP as an internal standard, the cRMP was optimized, covering sample preparation, calibration, and LC-MS/MS analysis. The method performance was validated across several parameters, including precision, accuracy, specificity, detection limits, and matrix effects. Clinical applicability was further assessed through the establishment of reference intervals for healthy newborns. The developed cRMP exhibited a linear range of 1.00 to 80.00 ng/mL for 17α-OHP, with detection and quantification limits of 0.14 ng/mL and 0.52 ng/mL, respectively. Inter- and intraday precision demonstrated coefficients of variation within 1.27 to 5.69%. The recovery rates and matrix effects were well within acceptable limits, ensuring method reliability. Clinical application showed distinct reference intervals for healthy newborns that were unaffected by sex but influenced by weight and gestational age. This method significantly enhances CAH diagnostic accuracy in newborns, providing a valuable tool for clinical laboratories and improving newborn screening program standardization and traceability.

Keywords:  17α-Hydroxyprogesterone; Congenital adrenal hyperplasia; Dried blood spots; Liquid chromatography tandem mass spectrometry; Newborn screening

DOI:  https://doi.org/10.1007/s00216-024-05411-9
Rapid Commun Mass Spectrom. 2024 Sep 15. 38(17): e9856

Broad-spectrum and sensitive screening of more than 1000 compounds in equine urine using liquid chromatography/high-resolution mass spectrometry.

Taiga Uchida, Takaya Kisugi, Hideaki Ishii, Masayuki Yamada, Kenji Kinoshita, Gary Ngai-Wa Leung.

RATIONALE: To uphold the integrity of horseracing and equestrian sports, it is critical for an equine doping control laboratory to develop a comprehensive screening method to cover a wide range of target substances at the required detection levels in equine urine.
METHODS: The procedure involved the enzymatic hydrolysis of 3 mL urine samples followed by solid-phase extraction using HF Bond Elut C18 cartridge. The resulting extracts were then separated on a C18 reversed-phase column and analyzed using liquid chromatography/high-resolution mass spectrometry (LC/HRMS) in both electrospray ionization positive and negative modes in two separate injections. The analytical data were obtained in full scan and product ion scan (PIS) modes in an 11 min LC run.
RESULTS: The method can detect 1011 compounds (in both positive and negative ion modes). Over 95% of the target compounds have limits of detections (LODs) ≤10 ng/mL, and more than 50% of the LODs are ≤0.5 ng/mL. The lowest LOD can reach down to 0.01 ng/mL. The applicability of the method was demonstrated by the successful detection of prohibited substances in overseas and domestic equine urine samples.
CONCLUSIONS: We have successfully developed a regular screening method for equine urine samples that can detect more than 1000 compounds at sub-ppb levels in both positive and negative ion modes with full scan and PIS using LC/HRMS. Furthermore, this method can theoretically be expanded to accommodate an unlimited number of prohibited substances in full-scan mode.

DOI: https://doi.org/10.1002/rcm.9856
Anal Chem. 2024 Jul 04.

Efficient Strategy for Characterization and Quantification of Polyunsaturated Lipids by Microwave-Assisted MMPP Epoxidation.

Longhui Huang, Minhan Huang, Ting Zhou.

Lipids play integral roles in biological processes, with carbon-carbon double bonds (C═C) markedly influencing their structure and function. Precise characterization and quantification of unsaturated lipids are crucial for understanding lipid physiology and discovering disease biomarkers. However, using mass spectrometry for these purposes presents significant challenges. In this study, we developed a microwave-assisted magnesium monoperoxyphthalate hexahydrate (MMPP) epoxidation reaction, coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS), to analyze unsaturated lipids. Microwave irradiation expedited the MMPP epoxidation, achieving complete derivatization in 10 min without byproducts. A diagnostic ion pair, displaying a 16 Da mass difference, effectively identified the location of the C═C bond in mass spectra. Microwave irradiation also significantly facilitated the epoxidation reaction of polyunsaturated lipids, achieving yields greater than 85% and yielding a complete epoxidation product. This simplifies chromatographic separation and aids in accurate quantification. Additionally, a purification process was implemented to remove excess derivatization reagents, significantly reducing mass spectrometry response suppression and enhancing analytical reproducibility. The method's effectiveness was validated by analyzing unsaturated lipids in rat plasma from a type I diabetes model. We quantified nine unsaturated lipids and characterized 42 fatty acids and glycerophospholipids. The results indicated that unsaturated fatty acids increased in diabetic plasma while unsaturated glycerophospholipids decreased. Furthermore, the relative abundances of Δ9/Δ11 isomer pairs also exhibited a close association with diabetes. In conclusion, microwave-assisted MMPP epoxidation coupled with LC-MS/MS provides an effective strategy for characterization and quantification of polyunsaturated lipids, offering deeper insight into the physiological impact of unsaturated lipids in related diseases.

DOI: https://doi.org/10.1021/acs.analchem.4c00410
Anal Chim Acta. 2024 Aug 08. pii: S0003-2670(24)00612-3. [Epub ahead of print]1316 342811

Ammonium bicarbonate buffers combined with hybrid surface technology columns improve the peak shape of strongly tailing lipids.

Jenny M Nilsson, David Balgoma, Curt Pettersson, Hans Lennernäs, Femke Heindryckx, Mikael Hedeland.

   BACKGROUND: Lipids such as phosphatidic acids (PAs) and cardiolipins (CLs) present strongly tailing peaks in reversed phase liquid chromatography, which entails low detectability. They are usually analyzed by hydrophilic interaction liquid chromatography (HILIC), which hampers high-throughput lipidomics. Thus, there is a great need for improved analytical methods in order to obtain a broader coverage of the lipidome in a single chromatographic method. We investigated the effect of ammonium bicarbonate (ABC) on peak asymmetry and detectability, in comparison with ammonium formate (AFO) on both a conventional BEH C18 column and an HST-CSH C18 column.
RESULTS: The combination of 2.5 mM ABC buffer pH 8 with an HST-CSH C18 column produced significantly improved results, reducing the asymmetry factor at 10 % peak height of PA 16:0/18:1 from 8.4 to 1.6. Furthermore, on average, there was up to a 54-fold enhancement in the peak height of its [M - H]- ion compared to AFO and the BEH C18 column. We confirmed this beneficial effect on other strongly tailing lipids, with accessible phosphate moieties e.g., cardiolipins, phosphatidylinositol phosphate, phosphatidylinositol bisphosphate, phosphorylated ceramide and phosphorylated sphingosine. Furthermore, we found an increased detectability of phospho- and sphingolipids up to 28 times in negative mode when using an HST-CSH C18 column. The method was successfully applied to mouse liver samples, where previously undetected endogenous phospholipids could be analyzed with improved chromatographic separation.
SIGNIFICANCE: In conclusion, the use of 2.5 mM ABC substantially improved the peak shape of PAs and enhanced the detectability of the lipidome in negative mode on an RPLC-ESI-Q-TOF-MS system on both BEH C18 and HST-CSH C18 columns. This method provides a wider coverage of the lipidome with one single injection for future lipidomic applications in negative mode.

Keywords:  Ammonium bicarbonate; Asymmetry factor; Cardiolipins; Chromatographic peak shape; Lipids; Phosphatidic acid

DOI:  https://doi.org/10.1016/j.aca.2024.342811
Clin Chim Acta. 2024 Jun 28. pii: S0009-8981(24)02089-8. [Epub ahead of print]561 119837

Quantification of treprostinil concentration in rat and human using a novel validated and rapid liquid chromatography-tandem mass spectrometry method: Experimental and clinical applications in ischemia-reperfusion injury.

Gina M Gallucci, Mariam Oladepo Agbabiaka, Meiwen Ding, Reginald Gohh, Nisanne S Ghonem.

  Treprostinil (Remodulin®) is a Food and Drug Administration (FDA) approved prostacyclin analog to treat pulmonary arterial hypertension. Recently, treprostinil has been investigated to reduce ischemia-reperfusion injury (IRI) during transplantation, which currently has no approved treatment. A validated analytical method is necessary to measure treprostinil concentrations in biological specimens. Here, a novel, sensitive, and specific method to measure treprostinil concentrations in rat serum, human serum, and human plasma has been developed using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Biological samples were processed by protein precipitation before chromatography and 6-keto Prostaglandin F1α-d4 was used as an internal standard. A gradient method was established with a total run time of 4 min. The assay was linear over the range of 0.25-75.0 ng/ml with accuracy (92.97-107.87 %), intra-assay precision (1.16-3.34 %), and inter-assay precision (1.11-4.58 %) in all biological matrices, which are within FDA acceptance criteria. No significant variation in treprostinil or 6-keto Prostaglandin F1α-d4 concentrations were observed under the investigated storage conditions. This novel, sensitive, and specific LC/MS-MS method is cost-effective and suitable for measuring treprostinil concentrations in animal studies and human biological samples for clinical applications.

Keywords:  Ischemia-reperfusion Injury; Kidney transplantation; Liquid chromatography-mass spectrometry; Prostacyclin; Treprostinil

DOI:  https://doi.org/10.1016/j.cca.2024.119837
J Pharm Biomed Anal. 2024 Jun 21. pii: S0731-7085(24)00361-3. [Epub ahead of print]248 116321

Bioanalytical validation and clinical application of a liquid chromatography-tandem mass spectrometry method for the quantification of 3-orthomethyldopa, 5-hydroxytryptophan, 5-hydroxyindolacetic acid and homovanillic acid in human cerebrospinal fluid.

Ignacio Bressán, Ornella Fracalossi Martínez, María Agustina Astolfo.

  Inherited disorders of monoamine neurotransmitters are a subset of inborn errors of metabolism affecting biochemical pathways of catecholamines, serotonin or their enzymatic cofactors. Usually, their clinical presentation is similar to those of other common neurological syndromes. For this reason, they are frequently under-recognized and misdiagnosed. Because cerebrospinal fluid concentration of catecholamine metabolites (3-orthomethyldopa and homovanillic acid) and serotonin metabolites (5-hydroxytryptophan and 5-hydroxyindolacetic acid) presents a direct correlation with their brain levels, analysis of this group of compounds is critical to reach an accurate diagnosis. Although there are several published liquid chromatography-based bioanalytical methods for the quantification of these compounds, most of them present disadvantages, making their application difficult to implement in routine clinical practice. In this study, a rapid and simple UHPLC-MS/MS method for simultaneous quantification of 3-orthomethyldopa, 5-hydroxytryptophan, 5-hydroxyindolacetic acid and homovanillic acid in human cerebrospinal fluid was validated. All the evaluated performance parameters, including linearity, carryover, accuracy and precision (within and between-day), lower limit of quantitation, recovery, matrix effect and stability under different conditions met the acceptance criteria from international guidelines. Additionally, 10 human cerebrospinal fluid samples collected via lumbar puncture from 10 pediatric patients were quantified using the validated method to assess its clinical application and diagnostic utility for inherited monoamine neurotransmitter metabolism.

Keywords:  3-orthomethyldopa; 5-hydroxyindolacetic acid; 5-hydroxytryptophan; Cerebrospinal fluid; Homovanillic acid; LC-MS/MS

DOI:  https://doi.org/10.1016/j.jpba.2024.116321
J Chem Inf Model. 2024 Jul 03.

Predicting Collision Cross-Section Values for Small Molecules through Chemical Class-Based Multimodal Graph Attention Network.

Cheng Wang, Chuang Yuan, Yahui Wang, Yuying Shi, Tao Zhang, Gary J Patti.

Libraries of collision cross-section (CCS) values have the potential to facilitate compound identification in metabolomics. Although computational methods provide an opportunity to increase library size rapidly, accurate prediction of CCS values remains challenging due to the structural diversity of small molecules. Here, we developed a machine learning (ML) model that integrates graph attention networks and multimodal molecular representations to predict CCS values on the basis of chemical class. Our approach, referred to as MGAT-CCS, had superior performance in comparison to other ML models in CCS prediction. MGAT-CCS achieved a median relative error of 0.47%/1.14% (positive/negative mode) and 1.40%/1.63% (positive/negative mode) for lipids and metabolites, respectively. When MGAT-CCS was applied to real-world metabolomics data, it reduced the number of false metabolite candidates by roughly 25% across multiple sample types ranging from plasma and urine to cells. To facilitate its application, we developed a user-friendly stand-alone web server for MGAT-CCS that is freely available at https://mgat-ccs-web.onrender.com. This work represents a step forward in predicting CCS values and can potentially facilitate the identification of small molecules when using ion mobility spectrometry coupled with mass spectrometry.

DOI: https://doi.org/10.1021/acs.jcim.3c01934
Cell Rep Methods. 2024 Jun 26. pii: S2667-2375(24)00159-0. [Epub ahead of print] 100803

PANAMA-enabled high-sensitivity dual nanoflow LC-MS metabolomics and proteomics analysis.

Weiwei Lin, Fatemeh Mousavi, Benjamin C Blum, Christian F Heckendorf, Matthew Lawton, Noah Lampl, Ryan Hekman, Hongbo Guo, Mark McComb, Andrew Emili.

  High-sensitivity nanoflow liquid chromatography (nLC) is seldom employed in untargeted metabolomics because current sample preparation techniques are inefficient at preventing nanocapillary column performance degradation. Here, we describe an nLC-based tandem mass spectrometry workflow that enables seamless joint analysis and integration of metabolomics (including lipidomics) and proteomics from the same samples without instrument duplication. This workflow is based on a robust solid-phase micro-extraction step for routine sample cleanup and bioactive molecule enrichment. Our method, termed proteomic and nanoflow metabolomic analysis (PANAMA), improves compound resolution and detection sensitivity without compromising the depth of coverage as compared with existing widely used analytical procedures. Notably, PANAMA can be applied to a broad array of specimens, including biofluids, cell lines, and tissue samples. It generates high-quality, information-rich metabolite-protein datasets while bypassing the need for specialized instrumentation.

Keywords:  CP: biotechnology; CP: metabolism; SPME; integrated omics; metabolomics; nLC-MS; proteomics

DOI:  https://doi.org/10.1016/j.crmeth.2024.100803
Se Pu. 2024 Jul;42(7): 669-680

[Research progress of deep learning applications in mass spectrometry imaging data analysis].

Dong-Dong Huang, Xin-Yu Liu, Guo-Wang Xu.

  Mass spectrometry imaging (MSI) is a promising method for characterizing the spatial distribution of compounds. Given the diversified development of acquisition methods and continuous improvements in the sensitivity of this technology, both the total amount of generated data and complexity of analysis have exponentially increased, rendering increasing challenges of data postprocessing, such as large amounts of noise, background signal interferences, as well as image registration deviations caused by sample position changes and scan deviations, and etc. Deep learning (DL) is a powerful tool widely used in data analysis and image reconstruction. This tool enables the automatic feature extraction of data by building and training a neural network model, and achieves comprehensive and in-depth analysis of target data through transfer learning, which has great potential for MSI data analysis. This paper reviews the current research status, application progress and challenges of DL in MSI data analysis, focusing on four core stages: data preprocessing, image reconstruction, cluster analysis, and multimodal fusion. The application of a combination of DL and mass spectrometry imaging in the study of tumor diagnosis and subtype classification is also illustrated. This review also discusses trends of development in the future, aiming to promote a better combination of artificial intelligence and mass spectrometry technology.

Keywords:  data analysis; deep learning; mass spectrometry imaging (MSI); neural network

DOI:  https://doi.org/10.3724/SP.J.1123.2023.10035
J Pharm Biomed Anal. 2024 Jun 24. pii: S0731-7085(24)00362-5. [Epub ahead of print]248 116322

A rapid LC-MS/MS method for the simultaneous quantification of ivacaftor, lumacaftor, elexacaftor, tezacaftor, hexyl-methyl ivacaftor and ivacaftor carboxylate in human plasma.

Yi Zheng, Steeve Rouillon, Mohamed Khemakhem, David Balakirouchenane, Gabrielle Lui, Seef Abdalla, Mohammed Rohi Sanoufi, Lucie Sauvaitre, Laure Thebault, Déborah Hirt, Jean-Marc Treluyer, Inès Gana, Sihem Benaboud, Léo Froelicher-Bournaud.

  Cystic fibrosis is one of the most common genetic diseases among caucasian population. This disease is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene encoding for the CFTR protein. Lumacaftor, elexacaftor, tezacaftor, and ivacaftor were currently used as the treatment to Cystic fibrosis. In this study, we describe a new method for the simultaneous quantification of four molecules: lumacaftor, elexacaftor, tezacaftor, and ivacaftor, alongside two metabolites of ivacaftor, specifically hexyl-methyl ivacaftor and ivacaftor carboxylate by liquid chromatography-tandem mass spectrometry. This method holds significant utility for therapeutic drug monitoring and the optimization of treatments related to CFTR modulators. Molecules were extracted from 100 µL of plasma by a simple method of protein precipitation using acetonitrile. Following extraction, chromatographic separation was carried out by reverse chromatography on a C18 analytical column, using a gradient elution of water (0.05 % formic acid, V/V) and acetonitrile (0.05 % formic acid, V/V). The run time was 7 minutes at a flow rate of 0.5 mL/min. After separation, molecules were detected by electrospray ionization on a Xevo TQD triple-quadrupole-mass-spectrometer (Waters®, Milford, USA). The calibration range were: 0.053-20.000 mg/L for elexacaftor, tezacaftor and lumacaftor, 0.075-14.000 mg/L for ivacaftor, and 0.024-6.500 mg/L for hexyl-methyl ivacaftor and ivacaftor carboxylate. The proposed method underwent throughout validation demonstrating satisfactory precision (inter- and intra-day coefficients of variation less than 14.3 %) and a good accuracy (inter- and intra-day bias ranging between -13.7 % and 14.7 %) for all the analytes. The presented method for the simultaneous quantification of CFTR modulators and their metabolites in human plasma has undergone rigorous validation process yielding good results including strong precision and accuracy for all analytes. This method has been effectively used in routine analytical analysis and clinical investigations within our laboratory.

Keywords:  CFTR modulators; Cystic fibrosis; LC-MS/MS; Therapeutic drug monitoring

DOI:  https://doi.org/10.1016/j.jpba.2024.116322
Mass Spectrom Rev. 2024 Jul 03.

Advances in targeted liquid chromatography-tandem mass spectrometry methods for endocannabinoid and N-acylethanolamine quantification in biological matrices: A systematic review.

Khalisa Amir Hamzah, Natalie Turner, David Nichols, Luke J Ney.

  Liquid chromatography paired with tandem mass spectrometry (LC-MS/MS) is the gold standard in measurement of endocannabinoid concentrations in biomatrices. We conducted a systematic review of literature to identify advances in targeted LC-MS/MS methods in the period 2017-2024. We found that LC-MS/MS methods for endocannabinoid quantification are relatively consistent both across time and across biomatrices. Recent advances have primarily been in three areas: (1) sample preparation techniques, specific to the chosen biomatrix; (2) the range of biomatrices tested, recently favoring blood matrices; and (3) the breadth of endocannabinoid and endocannabinoid-like analytes incorporated into assays. This review provides a summary of the recent literature and a guide for researchers looking to establish the best methods for quantifying endocannabinoids in a range of biomatrices.

Keywords:  LC‐MS; anandamide; endocannabinoids; liquid chromatography; mass spectrometry

DOI:  https://doi.org/10.1002/mas.21897
Se Pu. 2024 Jul;42(7): 646-657

[Applications of chromatography in glycomics].

Yi Zheng, Cui-Yan Cao, Zhi-Mou Guo, Jing-Yu Yan, Xin-Miao Liang.

  Glycomics, an emerging "omics" technology that was developed after genomics and proteomics, is a discipline that studies the composition, structure, and functions of glycomes in cells, tissues, and organisms. Glycomics plays key roles in understanding the laws of major life activities, disease prevention and treatment, and drug quality control and development. At present, the structural analysis of glycans relies mainly on mass spectrometry. However, glycans have low abundance in biological samples. In addition, factors such as variable monosaccharide compositions, differences in glycosidic bond positions and modes, diverse branching structures, contribute to the complexity of the compositions and structures of glycans, posing great challenges to glycomics research. Liquid chromatography can effectively remove matrix interferences and enhance glycan separation to improve the mass spectrometric response of glycans. Thus, liquid chromatography and liquid chromatography coupled with mass spectrometry are important technical tools that have been actively applied to solve these problems; these technologies play indispensable roles in glycomics research. Different studies have highlighted similarities and differences in the applications of various types of liquid chromatography, which also reflects the versatility and flexibility of this technology. In this review, we first discuss the enrichment methods for glycans and their applications in glycomics research from the perspective of chromatographic separation mechanisms. We then compare the advantages and disadvantages of these methods. Some glycan-enrichment modes include affinity, hydrophilic interactions, size exclusion, and porous graphitized carbon adsorption. A number of newly developed materials exhibit excellent glycan-enrichment ability. We enumerate the separation mechanisms of reversed-phase high performance liquid chromatography (RP-HPLC), high performance anion-exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC), and porous graphitic carbon (PGC) chromatography in the separation and analysis of glycans, and describe the applications of these methods in the separation of glycans, glycoconjugates, and glyco-derivatives. Among these methods, HILIC and PGC chromatography are the most widely used, whereas HPAEC and RP-HPLC are less commonly used. The HILIC and RP-HPLC modes are often used for the separation of derived glycans. The ionization efficiency and detectability of glycans are significantly improved after derivatization. However, the derivatization process is relatively cumbersome, and byproducts inevitably affect the accuracy and completeness of the detection results. HPAEC and PGC chromatography exhibit good separation effects on nonderivative glycans, but issues related to the detection integrity of low-abundance glycans owing to their poor detection effect continue to persist. Therefore, the appropriate analytical method for a specific sample or target analyte or mutual verification must be selected. Finally, we highlight the research progress in various chromatographic methods coupled with mass spectrometry for glycomics analysis. Significant progress has been made in glycomics research in recent years owing to advancements in the development of chromatographic separation techniques. However, several significant challenges remain. As the development of novel separation materials and methods continues, chromatographic techniques may be expected to play a critical role in future glycomics research.

Keywords:  glycan enrichment; glycan separation; glycomics; liquid chromatography (LC)

DOI:  https://doi.org/10.3724/SP.J.1123.2023.12003
Anal Sci. 2024 Jul 05.

Measurement of atmospheric amines and aminoamides by column adsorption/extraction and hydrophilic liquid chromatography-electrospray-tandem mass spectrometry.

Kentaro Saeki, Kazuya Ikari, Shin-Ichi Ohira, Kei Toda.

  Sampling and chromatography-mass spectrometry methods were investigated to measure atmospheric amines and aminoamides. Amines and their amide derivatives play significant roles in new particle formation (NPF) in the atmosphere, especially diamines and aminoamides have higher NPF potentials compared to monoamines. For amine sampling, silica gel tube collection and formic acid extraction gave good overall recoveries (>93 ± 8%) for mono-, di-, tri-, tetramines, and aminoamides. Two chromatography methods were subjected to analyze the extracted amines. One involved direct analysis using hydrophilic interaction liquid chromatography with carboxyl or diol group functioned separation column (carboxyl-HILIC or diol-HILIC), and the other utilized derivatization with 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F) and subsequent reversed-phase chromatography (HPLC). Separated amines were detected by electrospray ionization and tandem mass spectrometry in both cases. DBD-F-HPLC method provided good sensitivity for mono- and all polyamines (limit of detection (LOD) < 4.6 nM, relative standard deviation (RSD) for 100 nM < 9.2%). However, aminoamides could not be detected by DBD-F-HPLC. Carboxyl-HILIC provided good sensitivities for mono- and diamines and aminoamides (LOD < 1.6 nM, RSD < 4.8%). Forest air measurement was performed and data obtained by carboxyl-HILIC and DBD-F-HPLC showed good agreement for 1,3-diaminopropane, 1,4-diaminobutane (putrescine) and 1,5-diaminopentane (cadaverine) (R2 = 0.9215-0.9739, n = 7-14). Carboxyl-HILIC method was the best for the amine analysis, and combination with silica gel tube sampling provides atmospheric monitoring available. The developed method can be used not only to study atmospheric chemistry of diamines and aminoamides but also to analyze flavor/odor of foods, flowers and wastes.

Keywords:  Atmospheric amines; DBD-F derivatization; HPLC–MS/MS; Hydrophilic interaction liquid chromatography; Polyamine

DOI:  https://doi.org/10.1007/s44211-024-00626-3
Chemosphere. 2024 Jul 02. pii: S0045-6535(24)01648-5. [Epub ahead of print] 142754

Development of a robust non-targeted analysis approach for fast identification of endocrine disruptors and their metabolites in human urine for exposure assessment.

Anca Baesu, Yong-Lai Feng.

  Endocrine disrupting chemicals are of concern because of possible human health effects, thus they are frequently included in biomonitoring studies. Current analytical methods are focused on known chemicals and are incapable of identifying or quantifying other unknown chemicals and their metabolites. Non-targeted analysis (NTA) methods are advantageous since they allow for broad chemical screening, which provides a more comprehensive characterization of human chemical exposure, and can allow elucidation of metabolic pathways for unknown chemicals. There are still many challenges associated with NTA, which can impact the results obtained. The chemical space, i.e., the group of known and possible compounds within the scope of the method, must clearly be defined based on the sample preparation, as this is critical in identifying chemicals with confidence. Data acquisition modes and mobile phase additives used with liquid chromatography coupled to high-resolution mass-spectrometry can affect the chemicals ionized and structural identification based on the spectral quality. In this study, a sample preparation method was developed using a novel clean-up approach with CarbonS cartridges, for endocrine-disrupting chemicals in urine, including new bisphenol A analogues and benzophenone-based UV filters, like methyl bis (4-hydroxyphenyl acetate). The study showed that data dependent acquisition (DDA) had a lower identification rate (40%) at low spiking levels, i.e., 1 ng/mL, compared to data independent acquisition (DIA) (57%), when Compound Discoverer was used. In DDA, more compounds were identified using Compound Discoverer, with an identification rate of 95% when ammonium acetate was compared to acetic acid (82%) as a mobile phase additive. TraceFinder software had an identification rate of 53% at 1 ng/mL spiking level using the DDA data, compared to 40% using the DIA data. Using the developed method, 2,4 bisphenol F was identified for the first time in urine samples. The results show how NTA can provide human exposure information for risk assessment and regulatory action but standardized reporting of procedures is needed to ensure study results are reproducible and accurate.

Keywords:  Endocrine disruptors; Identification accuracy; high-resolution mass spectrometry; human urine; non-targeted analysis

DOI:  https://doi.org/10.1016/j.chemosphere.2024.142754
Arch Toxicol. 2024 Jul 01.

Characterizing lipid constituents of B. moojeni snake venom: a comparative approach for chemical and biological investigations.

Nathalia Santos Carvalho, Viviani Nardini, Raul Moyses Veronezes, Jéssica Burlamaque Maciel, Amanda Cristina Trabuco, Mirian Félix De Carvalho, Caroline Fontanari, Marco Aurélio Sartim, Luiz Alberto Beraldo de Moraes, Lúcia Helena Faccioli.

  Snake venoms are complex mixtures majorly composed of proteins with well-studied biological effects. However, the exploration of non-protein components, especially lipids, remains limited despite their potential for discovering bioactive molecules. This study compares three liquid-liquid lipid extraction methods for both chemical and biological analyses of Bothrops moojeni snake venom. The methods evaluated include the Bligh and Dyer method (methanol, chloroform, water), considered standard; the Acunha method, a modification of the Bligh and Dyer protocol; and the Matyash method (MTBE/methanol/water), featuring an organic phase less dense than the aqueous phase. Lipidomic analysis using liquid chromatography with high-resolution mass spectrometry (LC-HRMS) system revealed comparable values of lipid constituents' peak intensity across different extraction methods. Our results show that all methods effectively extracted a similar quantity of lipid species, yielding approximately 17-18 subclasses per method. However, the Matyash and Acunha methods exhibited notably higher proportions of biologically active lipids compared to the Bligh and Dyer method, particularly in extracting lipid species crucial for cellular structure and function, such as sphingomyelins and phosphatidylinositol-phosphate. In conclusion, when selecting a lipid extraction method, it is essential to consider the study's objectives. For a biological approach, it is crucial to evaluate not only the total quantity of extracted lipids but also their quality and biological activity. The Matyash and Acunha methods show promise in this regard, potentially offering a superior option for extracting biologically active lipids compared to the Bligh and Dyer method.

Keywords:  Lipidomics; Liquid chromatography–tandem mass spectrometry (LC-MS/MS); Liquid–liquid extraction (LLE); Venom

DOI:  https://doi.org/10.1007/s00204-024-03809-z
J Chromatogr B Analyt Technol Biomed Life Sci. 2024 Jun 25. pii: S1570-0232(24)00228-9. [Epub ahead of print]1243 124219

Study on the correlation and difference of qualitative information among three types of UPLC-HRMS and potential generalization in metabolites annotation.

Zhongda Zeng, Jinfeng Huo, Yuxi Zhang, Yingjiao Shi, Zeying Wu, Qianxu Yang, Xiaodan Zhang.

  The variation of qualitative information among different types of mainstream hyphenated instruments of ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (UPLC-HRMS) makes data sharing and standardization, and further comparison of results consistency in metabolite annotation not easy to attain. In this work, a quantitative study of correlation and difference was first achieved to systematically investigate the variation of retention time (tR), precursor ion (MS1), and product fragment ions (MS2) generated by three typical UPLC-HRMS instruments commonly used in metabolomics area. In terms of the findings of systematic and correlated variation of tR, MS1, and MS2 between different instruments, a computational strategy for integrated metabolite annotation was proposed to reduce the influence of differential ions, which made full use of the characteristic (common) and non-common fragments for scoring assessment. The regular variations of MS2 among three instruments under four collision energy voltages of high, medium, low, and hybrid levels were respectively inspected with three technical replicates at each level. These discoveries could improve general metabolite annotation with a known database and similarity comparison. It should provide the potential for metabolite annotation to generalize qualitative information obtained under different experimental conditions or using instruments from various manufacturers, which is still a big headache in untargeted metabolomics. The mixture of standard compounds and serum samples with the addition of standards were applied to demonstrate the principle and performance of the proposed method. The results showed that it could be an optional strategy for general use in HRMS-based metabolomics to offset the difference in metabolite annotation. It has some potential in untargeted metabolomics.

Keywords:  Metabolite annotation; Standard components; UPLC-HRMS; Universal database; Untargeted metabolomics

DOI:  https://doi.org/10.1016/j.jchromb.2024.124219
Food Res Int. 2024 Aug;pii: S0963-9969(24)00655-0. [Epub ahead of print]190 114585

Investigating the etiology of Haff disease: Optimization and validation of a sensitive LC-MS/MS method for palytoxins analysis in directly associated freshwater and marine food samples from Brazil.

Milena Dutra Pierezan, Cristian Rafael Kleeman, Pedro Luiz Manique Barreto, Rodrigo Barcellos Hoff, Silvani Verruck.

  Haff disease typically develops after eating contaminated marine or freshwater species, especially fish. Despite still having an unknown etiology, recent reports have suggested its possible correlation with palytoxins. Therefore, the present work aimed to optimize and perform a validation of a sensitive method using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for the analysis of palytoxin and some of its analogs, with the main purpose of investigating their presence in marine and freshwater food samples associated with Haff disease in Brazil. The method optimization was performed using a central composite rotatable design and fish samples fortified with the palytoxin standard. Then, the optimized method was validated for different food matrices, including freshwater and marine fish, mollusks, and crustaceans. The sample preparation involved a solid-liquid extraction using methanol and water, solid-phase extraction using Strata-X cartridges, and on-column palytoxin oxidation. The detection of the main oxidized fragments (amino and amide aldehydes) was achieved by LC-MS/MS with electrospray ionization in positive mode, using a C18 column, as well as acetonitrile and water as mobile phases, both acidified with 0.1 % of formic acid. After optimization and validation, the etiological investigation involved the analysis of 16 Brazilian Haff disease-related food samples (in natura and leftover meals) from 2022. The method was demonstrated to be appropriate for quantitative analysis of freshwater and marine species. So far, it has proven to be one of the most sensitive methods related to palytoxin detection (LOD 10 μg/kg), being able to work in a range that includes the provisional ingestion limit (30 μg/kg). Regarding the Haff disease-related samples analysis, there is a strong indication of palytoxin contamination since the amino aldehyde (common fragment for all palytoxins) was detected in 15 of the 16 samples. Selected results were confirmed using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS).

Keywords:  Dark brown urine disease; Emergent biotoxins; Emergent disease; Foodborne disease; In silico prediction; LC-qTOF-MS; Mascarenotoxins; Ostreocins; Ovatoxins; Palytoxin-like; SPE; Solubility

DOI:  https://doi.org/10.1016/j.foodres.2024.114585
Analyst. 2024 Jul 02.

Probe oscillation control in tapping-mode scanning probe electrospray ionization for stabilization of mass spectrometry imaging.

Mengze Sun, Yoichi Otsuka, Maki Okada, Shuichi Shimma, Michisato Toyoda.

Mass spectrometry imaging (MSI) is used for visualizing the distribution of components in solid samples, such as biological tissues, and requires a technique to ionize the components from local areas of the sample. Tapping-mode scanning probe electrospray ionization (t-SPESI) uses an oscillating capillary probe to extract components from a local area of a sample with a small volume of solvent and to perform electrospray ionization of those components at high speed. MSI can be conducted by scanning the sample surface with a capillary probe. To ensure stable extraction and ionization for MSI, the probe oscillation during measurements must be understood. In this study, we examined the changes in oscillation amplitude and phase due to the interaction between the oscillating probe and the brain tissue section when the probe tip was dynamically brought close to the sample surface. The changes in the probe oscillation depended on the oscillation frequency and polarity of the bias voltage applied to the solvent because an electrostatic force shifted the frequency of the probe oscillation. These findings suggest that controlling the probe oscillation frequency is important for stabilizing MSI by t-SPESI.

DOI: https://doi.org/10.1039/d4an00712c
Anal Bioanal Chem. 2024 Jul 02.

Evaluation and clinical application of a bracketing calibration-based isotope dilution liquid chromatography-tandem mass spectrometry candidate reference measurement procedure for serum theophylline.

Yuanyuan Du, Qiaofang Yan, Min Zhan, Qiaoxuan Zhang, Di Huang, Pengwei Zhang, Jun Yan, Jianbing Wang, Xianzhang Huang, Liqiao Han.

  A candidate reference measurement procedure (RMP) for serum theophylline via isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed. With a single-step precipitation pretreatment and a 6-min gradient elution, the method achieved baseline separation of theophylline and its analogs on a C18-packed column. A bracketing calibration method was used to ensure repeatable signal intensity and high measurement precision. The intra-assay and inter-assay imprecisions were 1.06%, 0.84%, 0.72% and 0.47%, 0.41%, 0.25% at concentrations of 4.22 µg/mL (23.40 µmol/L), 8.45 µg/mL (46.90 µmol/L), and 15.21 µg/mL (84.43 µmol/L), respectively. Recoveries ranged from 99.35 to 102.34%. The limit of detection (LoD) was 2 ng/mL, and the lowest limit of quantification (LLoQ) was 5 ng/mL. The linearity range extended from 0.47 to 60 µg/mL (2.61-333.04 µmol/L). No ion suppression and carry-over (< 0.68%) were observed. The relative bias for this candidate RMP that participated in 2023 External Quality Control for Reference Laboratories (RELA) conducted by the International Federation of Clinical Chemistry (IFCC) was within a range of 0.17 to 0.93%. Furthermore, two clinical immunoassay systems were compared with this candidate RMP, demonstrating good correlations. The results of the Trueness Verification Plan indicate significant differences among routine systems, highlighting the need for standardization efforts. The developed candidate RMP for serum theophylline serves as a precise reference baseline for standardizing clinical systems and assigning values to reference materials.

Keywords:  Candidate reference measurement procedure; ID-LC-MS/MS; Standardization; Theophylline; Therapeutic drug monitoring; Trueness Verification Plan

DOI:  https://doi.org/10.1007/s00216-024-05415-5
J Chromatogr B Analyt Technol Biomed Life Sci. 2024 Jun 17. pii: S1570-0232(24)00220-4. [Epub ahead of print]1243 124211

Improved method for quantification of intact oxaliplatin by ultra high performance liquid chromatography-inductively coupled plasma mass spectrometry: Applications to clinical and speciation studies.

John Ho, Christian Hartinger, Mark McKeage, Catherine Han.

  Interest is increasing in the use of different liquid chromatography techniques coupled online to mass spectrometry for the quantification of platinum anticancer drugs in human plasma to inform cancer chemotherapy. We developed, validated and studied the application of a method for quantification of intact oxaliplatin in human plasma using ultra high performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (UHPLC-ICP-MS). Plasma samples were processed instantly after collection from patients to preserve oxaliplatin speciation by methanol-deproteinization, and storage of diluted supernatants (plasma:methanol 1:2 v/v) at -80 °C. UHPLC separation of intact oxaliplatin and internal standard (carboplatin) was achieved using a C18 column and linear gradient mobile phase (Mobile phase A: water-methanol (97:3 v/v), 0.075 mM sodium dodecyl sulfate, 9.79 nM thallium adjusted to pH 2.5 with trifluoromethanesulfonic acid; Mobile phase B: 100 % methanol (v/v)) with ICP-MS detection to monitor platinum and thallium at m/z 195 and 205, respectively. The limit of quantification was 50 nM in methanol-deproteinized diluted plasma (1:2 v/v). Linearity was established for calibration standards ranging from 50 to 500 nM made in methanol-deproteinized diluted plasma (1:2 v/v), and for dilution of higher concentration samples in blank matrix containing internal standard (final dilution 1:29 v/v). Intra-day and inter-day accuracy ranged from 96.8 to 103 % of nominal concentration and precision from 0.62 to 2.49 % coefficient of variation. Recovery was complete and a matrix effect confirmed the requirement for matrix-matched standards. Intact oxaliplatin was stable during storage for at least 473 days, and during analysis, in methanol-deproteinized diluted plasma (1:2 v/v). The method was applied to determining the plasma concentrations of intact oxaliplatin in patients undergoing cancer chemotherapy, and studies of oxaliplatin degradation in vitro. This improved method based on UHPLC-ICP-MS will allow more specific, efficient and reliable quantification of intact oxaliplatin in human plasma.

Keywords:  Cancer chemotherapy; Human plasma; Inductively coupled plasma mass spectrometry; Oxaliplatin; Ultra high performance liquid chromatography

DOI:  https://doi.org/10.1016/j.jchromb.2024.124211
Comput Biol Med. 2024 Jul 01. pii: S0010-4825(24)00898-9. [Epub ahead of print]179 108813

Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data.

Chen Zhao, Kuan-Jui Su, Chong Wu, Xuewei Cao, Qiuying Sha, Wu Li, Zhe Luo, Tian Qing, Chuan Qiu, Lan Juan Zhao, Anqi Liu, Lindong Jiang, Xiao Zhang, Hui Shen, Weihua Zhou, Hong-Wen Deng.

   BACKGROUND: Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. The integration of whole-genome sequencing (WGS) data with metabolomics data has emerged as a promising approach to enhance the accuracy of data imputation in metabolomics studies.
METHOD: In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. Our approach utilizes a multi-scale variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing metabolomics data imputation. By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information.
RESULTS: We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. Using 35 template metabolites derived burden scores, PGS and LD-pruned SNPs, the proposed methods achieved R2-scores > 0.01 for 71.55 % of metabolites.
CONCLUSION: The integration of WGS data in metabolomics imputation not only improves data completeness but also enhances downstream analyses, paving the way for more comprehensive and accurate investigations of metabolic pathways and disease associations. Our findings offer valuable insights into the potential benefits of utilizing WGS data for metabolomics data imputation and underscore the importance of leveraging multi-modal data integration in precision medicine research.

Keywords:  Imputation; Metabolomics; Multi-scale; Variational autoencoder; Whole genome sequencing

DOI:  https://doi.org/10.1016/j.compbiomed.2024.108813
PLoS One. 2024 ;19(7): e0306202

uafR: An R package that automates mass spectrometry data processing.

Chase A Stratton, Yvonne Thompson, Konilo Zio, William R Morrison, Ebony G Murrell.

Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.

DOI: https://doi.org/10.1371/journal.pone.0306202
Anal Sci Adv. 2024 Jun;5(5-6): e2400002

Targeted and untargeted metabolomics and lipidomics in dried blood microsampling: Recent applications and perspectives.

Pauline Couacault, Dennisse Avella, Sara Londoño-Osorio, Ana S Lorenzo, Ana Gradillas, Olli Kärkkäinen, Elizabeth Want, Michael Witting.

  Blood microsampling (BµS) offers an alternative to conventional methods that use plasma or serum for profiling human health, being minimally invasive and cost effective, especially beneficial for vulnerable populations. We present a non-systematic review that offers a synopsis of the analytical methods, applications and perspectives related to dry blood microsampling in targeted and untargeted metabolomics and lipidomics research in the years 2022 and 2023. BµS shows potential in neonatal and paediatric studies, therapeutic drug monitoring, metabolite screening, biomarker research, sports supervision, clinical disorders studies and forensic toxicology. Notably, dried blood spots and volumetric absorptive microsampling options have been more extensively studied than other volumetric technologies. Therefore, we suggest that a further investigation and application of the volumetric technologies will contribute to the use of BµS as an alternative to conventional methods. Conversely, we support the idea that harmonisation of the analytical methods when using BµS would have a positive impact on its implementation.

Keywords:  LC–MS analysis; blood microsampling; dried blood; lipidomics; metabolomics; targeted and untargeted

DOI:  https://doi.org/10.1002/ansa.202400002