bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2022‒12‒18
29 papers selected by
Sofia Costa

  1. Anal Chem. 2022 Dec 15.
      Liquid chromatography (LC)-mass spectrometry (MS)/MS lipidomic normalization is generally performed by equalizing pre-extraction sample materials or via DNA or protein pre-quantitation methods, which have known measurement inaccuracies. We propose the use of the sulfo-phospho-vanillin assay (SPVA), a total lipid colorimetric analysis, as a pre-quantitation method to normalize lipids in lipidomic LC-MS/MS applications. The assay has been applied to a 300 μL well volume in a 96-well plate and tested using Avanti total lipid standards of porcine brain and E. coli. Assay parameters for lipid sample volume, sulfuric acid, vanillin/phosphoric acid, post-reaction incubation time, and wavelength are optimized for robust application to biologically sourced lipid samples. Standard test samples were prepared using three concentrations covering approximately 100 μg/mL range. The optimized assay yielded test sample errors less than 10%, indicating a precise and accurate assay performance. The test samples were then analyzed by LC-MS/MS and normalized using SPVA pre-quantitation and pseudo-mass normalization. The detected lipids showed smaller standard deviations and greater relative concentration differences compared to the pseudo-mass normalized lipids, showing promise as a normalization method.
  2. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Dec 05. pii: S1570-0232(22)00467-6. [Epub ahead of print]1214 123562
      Benzalkyldimethylammonium (or benzalkonium; BACs), alkyltrimethylammonium (ATMACs), and dialkyldimethylammonium compounds (DDACs) have been widely used for over six decades as disinfectants, especially during the COVID-19 pandemic. Here we describe methods for the determination of 7 BACs, 6 ATMACs, 6 DDACs, 8 BAC metabolites, and the structurally similar quaternary ammonium compound (QAC) herbicides diquat, paraquat, and difenzoquat in human serum and urine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methods were optimized using isotopically labelled internal standards and solid-phase extraction with weak cation-exchange cartridges. We separated diquat and paraquat chromatographically using a mixed-mode LC column, and BACs, ATMACs, DDACs, difenzoquat, and BAC metabolites using reversed-phase (C8 and C18) LC columns. Method limits of detection (MLODs) and quantification (MLOQs) were 0.002-0.42 and 0.006-1.40 ng/mL, respectively. Recoveries of all analytes fortified at 1, 5, and 20 ng/mL concentrations in serum and urine matrices were 61-129%, with standard deviations of 0-20%. Repeated analysis of similarly fortified serum and urine samples yielded intra-day and inter-day variations of 0.22-17.4% and 0.35-17.3%, respectively. Matrix effects for analytes spiked into serum and urine matrices ranged from -27% to 15.4%. Analysis of real urine and serum samples revealed the presence of several QACs in human serum. Although no parent BACs were found in urine, we detected, for the first time, several ω-hydroxy and ω-carboxylic acid metabolites of BACs at average concentrations in the range of 0.05-0.35 ng/mL. The developed method is suitable for application in large-scale biomonitoring of human exposure to QACs and their metabolites in human serum and urine.
    Keywords:  Benzalkonium; Carboxylic benzalkonium; Disinfectant; Exposure; Paraquat; Quaternary ammonium compound; Serum; Urine
  3. J Chromatogr A. 2022 Dec 07. pii: S0021-9673(22)00898-6. [Epub ahead of print]1687 463707
      Comprehensive characterization of the lipidome remains a challenge requiring development of new analytical approaches to expand lipid coverage in complex samples. In this work, offline two-dimensional liquid chromatography-mass spectrometry was investigated for lipidomics from human plasma. Hydrophilic interaction liquid chromatography was implemented in the first dimension to fractionate lipid classes. Nine fractions were collected and subjected to a second-dimension separation utilizing 50 cm capillary columns packed with 1.7 µm C18 particles operated on custom-built instrumentation at 35 kpsi. Online coupling with time-of-flight mass spectrometry allowed putative lipid identification from precursor-mass based library searching. The method had good orthogonality (fractional coverage of ∼40%), achieved a peak capacity of approximately 1900 in 600 min, and detected over 1000 lipids from a 5 µL injection of a human plasma extract while consuming less than 3 mL of solvent. The results demonstrate the expected gains in peak capacity when employing long columns and two-dimensional separations and illustrate practical approaches for improving lipidome coverage from complex biological samples.
    Keywords:  Capillary liquid chromatography; Lipidomics; Nanoscale liquid chromatography; Two-dimensional chromatography; Ultra-high pressure liquid chromatography
  4. Molecules. 2022 Dec 06. pii: 8604. [Epub ahead of print]27(23):
      Palbociclib and abemaciclib are two cyclin-dependent kinases 4 and 6 used for breast cancer treatment. Levels of these medicines present a significant interindividual variability, so monitoring those concentrations might be necessary in therapy. Most of the methods presented so far in the literature use simple protein precipitation of plasma proteins as sample preparation method followed by direct injection of the supernatant into the LC instrument, preceded or not by a simple filtration step. Within that approach, the probability of injecting proteins in the chromatographic system is increased. With the purpose of obtaining a cleaner extract of the drugs, we developed and validated a simple and accurate LC-MS method for determining palbociclib and abemaciclib in human plasma. Solid phase extraction (SPE) using Oasis PRiME HLB® cartridges was used for plasma sample preparation. The method provided clean extracts with a recovery extraction higher than 85% for both compounds. Separation was achieved by high-performance liquid chromatography (HPLC), using a C18 (4.6 × 50 mm) column, with a gradient elution of ammonium acetate/acetic acid-acetonitrile as the mobile phase. Detection was performed by mass spectrometry (MS) in single ion recording (SIR) mode. Intra-day and inter-day precision data for both analytes were 3.8-7.2% and 3.6-7.4%, respectively. Calibration curves were both linear between 2 and 400 ng/mL with a correlation coefficient higher than 0.998. The LC-MS method can be used to quantify the drugs in human plasma in routine analysis. The method proved to be useful in determining real plasma levels in patients involved in cancer therapy. Drug concentrations were determined in a 10 min run-time, including re-equilibration of the column.
    Keywords:  LC-MS; SPE; abemaciclib; human plasma; palbociclib
  5. Int J Mol Sci. 2022 Nov 24. pii: 14691. [Epub ahead of print]23(23):
      Steroid analysis in clinical laboratories is dominated by immunoassays (IAs) that have a high sample turnover but are inherently limited in trueness, precision, and sensitivity. Liquid chromatography coupled to mass spectrometry (LC-MS/MS) has proved to be a far more capable tool, delivering better sensitivity, specificity, and the possibility of parallel analysis of multiple steroids and metabolites, providing the endocrinologist with more reliable and comprehensive diagnostic information. An LC-MS/MS assay with gradient elution over less than eight minutes and a one-step sample preparation combining protein precipitation with phospholipid removal of off-line solid-phase extraction was developed and validated. It allowed the quantification of 11-deoxycorticosterone (11-DOC), 11-deoxycortisol (11-DF), 17-OH-progesterone (17P), 21-deoxycortisol (21-DF), androstenedione (ANDRO), aldosterone (ALDO), corticosterone (CC), cortisol (CL), cortisone (CN), dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate (DHEAS), dihydrotestosterone (DHT), estradiol (E2), progesterone (PROG), and testosterone (TES) in human serum. Interday imprecision was generally better than 15%, trueness was proven by recovery experiments with ISO 17034-certified reference materials, proficiency testing (UK NEQAS), and measuring serum reference standards. In-house comparison against IVD-CE-certified immunoassays (IA) for 17P, ANDRO, CL, DHEAS, E2, PROG, and TES was conducted by assessing leftover routine patient samples and purpose-built patient serum pools. None of the compared routine IAs were meeting the standards of the LC-MS/MS. Insufficient overall comparability was found for ANDRO and 17P (mean bias > +65%). Accuracy limitations at lower concentrations were present in IAs for PROG, E2, and TES.
    Keywords:  LC-MS/MS; endocrinology; laboratory medicine; steroid measurement
  6. Biostatistics. 2022 Dec 12. 24(1): 140-160
      The process of identifying and quantifying metabolites in complex mixtures plays a critical role in metabolomics studies to obtain an informative interpretation of underlying biological processes. Manual approaches are time-consuming and heavily reliant on the knowledge and assessment of nuclear magnetic resonance (NMR) experts. We propose a shifting-corrected regularized regression method, which identifies and quantifies metabolites in a mixture automatically. A detailed algorithm is also proposed to implement the proposed method. Using a novel weight function, the proposed method is able to detect and correct peak shifting errors caused by fluctuations in experimental procedures. Simulation studies show that the proposed method performs better with regard to the identification and quantification of metabolites in a complex mixture. We also demonstrate real data applications of our method using experimental and biological NMR mixtures.
    Keywords:  Chemical shift; NMR metabolomics; Regularized regression; Spectral data
  7. Molecules. 2022 Nov 23. pii: 8139. [Epub ahead of print]27(23):
      Platinum-based cytostatic drugs are one of the most widely used cancer treatments. They are excreted via the urinary tract and can reach the environment through wastewater, posing a risk to human health due to their side effects. Four identification and quantification techniques, including liquid chromatography (LC) separation coupled to (i) a diode array ultraviolet (UV(DAD)) (ii), mass spectrometer in single ion monitoring mode (LC-MS) and (iii) multiple reaction monitoring mode (LC-MS/MS) and (iv) derivatization with diethyldithiocarbamate prior to LC-MS/MS analysis, have been optimized and compared for the multiresidue determination of main platinized cytostatic drugs (cisplatin, carboplatin, and oxaliplatin) in urine samples. Parameters that affect the efficiency of the chromatographic separation and analytical determination of different methods (column, mobile phase, wavelength, precursor ions, fragmentor, and product ions) were optimized. Analytical features, such as matrix effect, sensitivity, precision, selectivity, and linearity, were calculated. In terms of selectivity, the derivatization technique was discarded since it was only applicable to the platinated sum. A high dilution of the sample with LC-UV(DAD) was needed to reduce the matrix effect. Overall, the LC-MS/MS method presented the best analytical features (% RSD ≤ 12.8%, R2 ≥ 0.991, or method-detection limits between 0.01-1 µg mL-1). The selected method was applied to the quantification of platinized cytostatic drugs in hospital urine samples from oncologic patients.
    Keywords:  LC-MS/MS; LC-UV(DAD); MRM mode; SIM mode; carboplatin; cisplatin; cytostatic drugs; oxaliplatin
  8. Int J Mol Sci. 2022 Nov 28. pii: 14864. [Epub ahead of print]23(23):
      The marked sexual dimorphism prevalent in inflammatory/autoimmune diseases is mostly due to sex hormone actions. One common eye disease that disproportionately affects women is dry eye. Thus, our aim was to optimise our highly sensitive liquid chromatography-tandem mass spectrometry method for steroid hormone quantification in tear fluid (TF). We used tears and matched serum samples from 10 heathy individuals. Estrone, estradiol testosterone, progesterone, androstenedione, and dehydroepiandrosterone, were quantified with an HPLC coupled with a Triple Quad 5500 MS. Estrone was measured in 80% of female and 20% of male TF samples (mean ± SD, 68.9 ± 62.2 pmol/L), whereas estradiol was undetectable in tears. Progesterone was identified in half of the female tear samples (2.91 ± 3.47 nmol/L) but in none of the male samples, whereas testosterone was quantifiable only in male tears (0.24 ± 0.1 nmol/L). TF hormone levels were, on average, from 1.4% to 55% of systemic values. Estrone, progesterone, and testosterone levels in tears correlated with the matching serum samples (r = 0.82, 0.79, and 0.85, respectively), but androstenedione and dehydroepiandrosterone showed no correlations. Our LC-MS/MS method could detect five out of the six steroid hormones studied in individual human TF samples and could therefore be used to analyse the role of sex steroids in eye diseases.
    Keywords:  estrogen; high performance liquid chromatography; mass spectrometry; steroid hormones; tear fluid; testosterone
  9. Front Mol Biosci. 2022 ;9 1021889
      Imaging mass spectrometry (MS) is becoming increasingly applied for single-cell analyses. Multiple methods for imaging MS-based single-cell metabolomics were proposed, including our recent method SpaceM. An important step in imaging MS-based single-cell metabolomics is the assignment of MS intensities from individual pixels to single cells. In this process, referred to as pixel-cell deconvolution, the MS intensities of regions sampled by the imaging MS laser are assigned to the segmented single cells. The complexity of the contributions from multiple cells and the background, as well as lack of full understanding of how input from molecularly-heterogeneous areas translates into mass spectrometry intensities make the cell-pixel deconvolution a challenging problem. Here, we propose a novel approach to evaluate pixel-cell deconvolution methods by using a molecule detectable both by mass spectrometry and fluorescent microscopy, namely fluorescein diacetate (FDA). FDA is a cell-permeable small molecule that becomes fluorescent after internalisation in the cell and subsequent cleavage of the acetate groups. Intracellular fluorescein can be easily imaged using fluorescence microscopy. Additionally, it is detectable by matrix-assisted laser desorption/ionisation (MALDI) imaging MS. The key idea of our approach is to use the fluorescent levels of fluorescein as the ground truth to evaluate the impact of using various pixel-cell deconvolution methods onto single-cell fluorescein intensities obtained by the SpaceM method. Following this approach, we evaluated multiple pixel-cell deconvolution methods, the 'weighted average' method originally proposed in the SpaceM method as well as the novel 'linear inverse modelling' method. Despite the potential of the latter method in resolving contributions from individual cells, this method was outperformed by the weighted average approach. Using the ground truth approach, we demonstrate the extent of the ion suppression effect which considerably worsens the pixel-cell deconvolution quality. For compensating the ion suppression individually for each analyte, we propose a novel data-driven approach. We show that compensating the ion suppression effect in a single-cell metabolomics dataset of co-cultured HeLa and NIH3T3 cells considerably improved the separation between both cell types. Finally, using the same ground truth, we evaluate the impact of drop-outs in the measurements and discuss the optimal filtering parameters of SpaceM processing steps before pixel-cell deconvolution.
    Keywords:  SpaceM; fluorescein diacetate (FDA); imaging mass spectrometry (imaging MS); ion suppression; pixel-cell deconvolution; spatial single-cell metabolomics
  10. Molecules. 2022 Nov 24. pii: 8186. [Epub ahead of print]27(23):
      Analytical methods for the quantification of the new 8-aminoquinoline antimalarial tafenoquine (TQ) in human blood, plasma and urine, and the 5,6-orthoquinone tafenoquine metabolite (5,6-OQTQ) in human plasma and urine have been validated. The procedure involved acetonitrile extraction of samples followed by ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). Chromatography was performed using a Waters Atlantis T3 column with a gradient of 0.1% formic acid and acetonitrile at a flow rate of 0.5 mL per minute for blood and plasma. Urine analysis was the same but with methanol containing 0.1% formic acid replacing acetonitrile mobile phase. The calibration range for TQ and 5,6-OQTQ in plasma was 1 to 1200 ng/mL, and in urine was 10 to 1000 ng/mL. Blood calibration range for TQ was 1 to 1200 ng/mL. Blood could not be validated for 5,6-OQTQ due to significant signal suppression. The inter-assay precision (coefficient of variation %) was 9.9% for TQ at 1 ng/mL in blood (n = 14) and 8.2% for TQ and 7.1% for 5,6-OQTQ at 1 ng/mL in plasma (n = 14). For urine, the inter-assay precision was 8.2% for TQ and 6.4% for 5,6-OQTQ at 10 ng/mL (n = 14). TQ and 5,6-OQTQ are stable in blood, plasma and urine for at least three months at both -80 °C and -20 °C. Once validated, the analytical methods were applied to samples collected from healthy volunteers who were experimentally infected with Plasmodium falciparum to evaluate the blood stage antimalarial activity of TQ and to determine the therapeutic dose estimates for TQ, the full details of which will be published elsewhere. In this study, the measurement of TQ and 5,6-OQTQ concentrations in samples from one of the four cohorts of participants is reported. Interestingly, TQ urine concentrations were proportional to parasite recrudescence times post dosing To our knowledge, this is the first description of a fully validated method for the measurement of TQ and 5,6-OQTQ quantification in urine.
    Keywords:  5,6-orthoquinone tafenoquine; analytical method; blood; malaria; plasma; tafenoquine; urine
  11. J Chromatogr A. 2022 Dec 05. pii: S0021-9673(22)00891-3. [Epub ahead of print]1687 463700
      In untargeted liquid chromatography‒mass spectrometry (LC‒MS) metabolomics studies, data preprocessing and metabolic pathway recognition are crucial for screening important pathways that are disturbed by diseases or restored by drugs. Here, we collected high-resolution mass spectrometry data of serum samples from 221 coronary heart disease (CHD) patients under two different chromatographic columns (BEH amide and C18 column) and evaluated the three commonly used software programs (XCMS, Progenesis QI, MarkerView) from four aspects (including signal drift, peak number, metabolite annotation and metabolic pathway enrichment). The results showed that the data preprocessed by the three software programs have different degrees of signal drift, but the StatTarget could improve the data quality to meet the data analysis requirement after correction. In addition, XCMS surpassed other software in detection of real chromatographic peaks and Progenesis QI was the best performer in terms of the number of metabolite annotation. XCMS and Progenesis QI showed different performance in pathway enrichment. However, metabolic pathways based on the combination of XCMS and Progenesis QI had a high coincidence with Progenesis QI. In addition, we also reported that C18 and amide columns were highly complementary and have great potential for cooperation in the context of metabolic pathways. In this study, the effects of different chromatographic columns and software pretreatments on metabolomics data were evaluated based on clinical large cohort samples, which will provide a reference for the metabolomics of clinical samples and guide subsequent mechanistic research.
    Keywords:  Data preprocessing; Metabolic pathway recognition; Metabolomics; Peak detection; Signal drift correction
  12. Anal Chem. 2022 Dec 15.
      Quantification of steroids possesses a crucial clinical value in early diagnosis and prognosis evaluation of various endocrine diseases. However, it is still challenging to realize feasible analysis of estrogens, androgens, progestogens, and corticoids within one single workflow. In this study, two derivatization reactions were newly designed for improvement: (1) acylation of phenolic hydroxyl on estrogens with isonicotinoyl chloride (INC) under the catalysis of 4-dimethylaminopyridine and (2) post-modification of oxime hydroxyl on hydroxylamine-pretreated ketosteroids with INC. Both reactions could conduct instantaneously at room temperature under aqueous conditions. Moreover, the resulting phenolic-INC and oxime-INC esters exhibited favorable MS responses. Through integrating these derivatization strategies with cold-induced phase separation technology, a feasible LC-MS/MS method was developed for simultaneous quantification of 15 multiclass steroids with proper sample consumption (50 μL serum), satisfying sensitivity (lower limit of quantitation at 0.01-5.00 ng/mL) and high throughput (40 min for sample-preparation). The practical applicability was tested by detecting 30 real samples from pregnant and non-pregnant women. The obtained results showed a good agreement with a previous validated methodology.
  13. Mass Spectrom Rev. 2022 Dec 16. e21826
      Chemical analysis by analytical instrumentation has played a major role in disease diagnosis, which is a necessary step for disease treatment. While the treatment process often targets specific organs or compounds, the diagnostic step can occur through various means, including physical or chemical examination. Chemically, the genome may be evaluated to give information about potential genetic outcomes, the transcriptome to provide information about expression actively occurring, the proteome to offer insight on functions causing metabolite expression, or the metabolome to provide a picture of both past and ongoing physiological function in the body. Mass spectrometry (MS) has been elevated among other analytical instrumentation because it can be used to evaluate all four biological machineries of the body. In addition, MS provides enhanced sensitivity, selectivity, versatility, and speed for rapid turnaround time, qualities that are important for instance in clinical procedures involving the diagnosis of a pediatric patient in intensive care or a cancer patient undergoing surgery. In this review, we provide a summary of the use of MS to evaluate biomarkers for newborn screening and cancer diagnosis. As many reviews have recently appeared focusing on MS methods and instrumentation for metabolite analysis, we sought to describe the biological basis for many metabolomic and additional omics biomarkers used in newborn screening and how tandem MS methods have recently been applied, in comparison to traditional methods. Similar comparison is done for cancer screening, with emphasis on emerging MS approaches that allow biological fluids, tissues, and breath to be analyzed for the presence of diagnostic metabolites yielding insight for treatment options based on the understanding of prior and current physiological functions of the body.
    Keywords:  cancer diagnosis; mass spectrometry; metabolomics; newborn screening
  14. Anal Bioanal Chem. 2022 Dec 12.
      The US National Institute of Standards and Technology (NIST) developed a Standard Reference Material® (SRM®) 3949 Folate Vitamers in Frozen Human Serum to replace SRM 1955 Homocysteine and Folate in Human Serum. The presence of increased endogenous levels of folic acid and 5-methyltetrahydrofolate (5mTHF) in SRM 3949, enhanced folate stability via addition of ascorbic acid, and inclusion of values for additional minor folates are improvements over SRM 1955 that should better serve the clinical folate measurement community. The new SRM contains folates at three levels. To produce SRM 3949, pilot sera were collected from 15 individual donors, 5 of whom were given a 400-µg folic acid supplement 1 h prior to blood draw to increase serum levels of 5mTHF and folic acid for the high-level material. To stabilize the folates, 0.5% (mass concentration) ascorbic acid was added as soon as possible after preparation of serum. These pilot sera were screened for five folates plus the pyrazino-s-triazine derivative of 4-α-hydroxy-5-methyltetrahydrofolate (MeFox) at the US Centers for Disease Control and Prevention (CDC) by isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS). Based on these results, a blending protocol was specified to obtain the three desired folate concentrations for SRM 3949. ID-LC-MS/MS analysis at the CDC and NIST was utilized to assign values for folic acid and 5mTHF, as well as several minor folates.
    Keywords:  Folate; Human serum; Liquid chromatography-tandem mass spectrometry; Reference material
  15. J Anal Methods Chem. 2022 ;2022 4819599
      Medical providers are increasingly confronted with clinical decision-making that involves (meth)amphetamines. And clinical laboratories need a sensitive, efficient assay for routine assessment of D- and L-isomers to determine the probable source of these potentially illicit analytes. This paper presents a validated method of D- and L-isomer detection in human oral fluid from an extract used for determination of a large oral fluid assay (63 analytes) on an older AB SCIEX 4000 instrument. Taken from the positive extract, D- and L-analytes were added. The method for extraction included addition of internal standard and a 2-step liquid-liquid extraction and dry-down step to concentrate and clean the samples. The samples were suspended in 50% MeOH in water, diluted with mobile phase, with separation and detection accomplished using LC-MS/MS to determine analyte concentration. Once samples were confirmed positive for (meth)amphetamine from the large oral fluid assay, they were further examined for the enantiomeric forms with 50 μl aliquots of the standards and samples of interest combined with 450 μl of D- and L-assay mobile phase, then analyzed using chiral column separation, and LC-MS/MS detection with standard curve spanning the range from 2.5 to 1000 ng/mL. The result is a sensitive and accurate detection of D- and L-isomers of amphetamine and methamphetamine in human oral fluid performed on an older model mass spectrometer (AB SCIEX 4000). The novelty of this assay is twofold (a) the 2-step liquid-liquid extraction and dry-down step to concentrate and clean the samples, and (b) its adoption characteristics as a reflex test from a large ODT panel without the need to invest in newer or expensive LC-MS/MS instruments. Finally, this assay also has potential to add a valuable option to high-throughput laboratories seeking a D- and L-testing alternative to urine drug testing methods.
  16. Cells. 2022 Dec 02. pii: 3900. [Epub ahead of print]11(23):
      Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
    Keywords:  MALDI MSI; Mass spectrometry imaging; biomarkers; diagnostics; drug distribution; microbial interactions; microbiology
  17. Anal Chem. 2022 Dec 15.
      Determining actinides in urine is vital for occupational exposure monitoring and radiological emergency response because of the toxicity and radiological dose effects of actinides on human health. Traditional radiochemistry analytical methods used to determine actinide concentrations in urine are time-consuming (sample analysis takes several days) and are hindered by a variety of technical and instrumentation-related obstacles. A high-throughput, fully automated, precise, and accurate in-line method was developed for determining five actinides (241Am, 239Pu, 237Np, 232Th, and 238U) at ng/L levels in urine using extraction chromatography combined with quadrupole inductively coupled plasma mass spectrometry (EC-ICP-MS). In this method, the five actinides were successfully separated with the required sensitivity, peak shape, and resolution using a simplified single Eichrom TRU column with a Dionex ICS-5000 system. The separated actinides were subsequently injected into an in-line PerkinElmer (PE) NexION 300D ICP-MS for quantitative determination. The sample-to-sample run time was 23 min for automatic chemical separation and quantification using only 0.5 mL of urine. The limits of detection (LOD) obtained using this method were 0.015, 0.022, 0.039, 4.5, and 2.4 ng/L for 241Am, 239Pu, 237Np, 232Th, and 238U, respectively. The method routinely had a chemical yield of >84% as well as a linearity (R2) coefficient of ≥0.999 for the calibrators. The method proved to be rapid, reliable, and effective for actinide quantification in urine and therefore is appropriate for radiological emergency response incidents.
  18. Front Chem. 2022 ;10 1062118
      Diacylglycerols (DAGs) are important lipid mediators in cellular signaling transduction and metabolism. Imbalanced production or consumption of DAGs has a negative impact on the physiological functions of the body. However, comprehensive monitoring of structurally diverse DAGs remains a daunting task due to the rapid metabolism and ion suppression characteristics in biofluids. These bottlenecks call for developing a method that enables sensitive quantification of DAGs in biological sample. In this work, a straightforward charge derivatization strategy was developed to insert a series of structure analogs charge label, i.e., N, N-dimethylglycine (DMG) and N, N-dimethylalanine (DMA), on the free hydroxyl group of the DAGs. Owing to the existence of tertiary amino groups in charge label, the mass spectrometry ionization response of the derivatized DAGs was significantly increased in comparison with traditional metal ion adducts. After charge derivatization, the specific neutral loss diagnostic ions (DMG, 103 Da and DMA, 117 Da) were captured by mass spectrometry. Then, the DMG/DMA-oriented paired multiple reaction monitoring methods based on the characteristic diagnostic ions of the derivatized DAGs have been developed as sensitive methods for the detection (detection limit = 16 aM) and quantification (quantification limit = 62.5 aM) of DAGs in serum. Moreover, the tagged 1,2-DAGs and 1,3-DAGs sn-isomers have been well separated on the reversed-phase column in combination with ultra-performance liquid chromatography. Finally, metabolic characterizations of the tagged DAGs were further explored in L-Arginine-induced acute pancreatitis mice and resveratrol treated model mice. The results indicated that 1,2-DAGs were increased in the serum of model mice relative to normal controls and resveratrol significantly altered this metabolic abnormality. The currently established DMG/DMA-oriented paired charge derivatization strategy is promising for depicting DAGs changes more accurately in metabolic studies of lipid-related diseases and accurately evaluating drug treatment strategies.
    Keywords:  UPLC-MS/MS; acute pancreatitis; charge derivatization; diacylglycerols; quantitation analysis
  19. Molecules. 2022 Dec 06. pii: 8607. [Epub ahead of print]27(23):
      Isoniazid and its metabolites are potentially associated with hepatotoxicity and treatment outcomes in patients who receive antituberculosis (TB) therapy. To further understand the pharmacokinetic profiles of these molecules, a method based on LC-MS/MS was developed to determine the concentration of these compounds in human plasma. Isoniazid, acetylisoniazid, and isonicotinic acid were directly analyzed, whereas hydrazine and acetylhydrazine were determined after derivatization using p-tolualdehyde. Chromatographic separation was conducted on reversed-phase C18 columns with gradient elution, and detection was carried out in multiple reaction monitoring mode. The calibration curves were linear with correlation coefficients (r) greater than 0.9947 for all analytes. The intra- and inter-day precision was less than 13.43%, and the accuracy ranged between 91.63 and 114.00%. The recovery and matrix effect of the analytes were also consistent (coefficient of variation was less than 9.36%). The developed method successfully quantified isoniazid and its metabolites in TB patients. The method has broad applications in clinical research, including isoniazid one-point-based therapeutic drug monitoring, genotype-phenotype association studies of isoniazid metabolic profile and isoniazid-induced hepatotoxicity, and the initial dose prediction of isoniazid using population pharmacokinetic modeling.
    Keywords:  NAT2; hydrazine; isoniazid; mass spectrometry; metabolic profiles; tuberculosis
  20. Molecules. 2022 Dec 06. pii: 8635. [Epub ahead of print]27(23):
      Organophosphate triesters are compounds widely used in industries and are ubiquitous in the environment, where they can be transformed into organophosphate diesters. Some organophosphate diesters are also used by industry. Several studies suggest organophosphate diesters can have toxic effects for reproduction, and hazardous and mutagenic properties. Due to the impact these compounds can have on marine biota and human beings through the consumption of fish and shellfish, it is necessary to study their presence in widely consumed seafood species. We therefore developed an analytical method for determining six of the most common organophosphate diesters in seafood. The procedure is based on the Quick, Easy, Cheap, Effective, Rugged and Safe extraction method and a solid phase extraction clean-up, followed by liquid chromatography coupled to high-resolution mass spectrometry. The method was optimised and validated for seafood with different lipid content, providing satisfactory relative recoveries (from 89 to 138%) and limits of detection (1.0-50 ng g-1 dry weight), as well as repeatability values (RSD% (n = 5, 100 ng g-1 (dry weight)) lower than 15%. Eight seafood species were analysed using this method and two organophosphate diesters were detected and quantified in all the samples, demonstrating the suitability of the method.
    Keywords:  QuEChERS; high-resolution mass spectrometry; liquid chromatography; organophosphate diesters; seafood; solid-phase extraction
  21. Molecules. 2022 Nov 25. pii: 8242. [Epub ahead of print]27(23):
      Determination of the fatty acid profile in milk samples is one of the most important in food analysis. There are many methodologies for FA determination. The conventional procedure for determining the FA composition of milk is isolation of fat or indirect methylation, trans-methylation, extraction of fatty acids, and analysis by gas chromatography. In this study, eight methods based on alkaline methylation were compared for the analysis of fatty acids in cow's milk. The response factors (RF) for GC analysis using FID were calculated. For most acids, RFs were close to 1, with the exception of short-chain fatty acids (C4:0-C8:0). To facilitate the selection of the method for the determination of fatty acids in milk samples, the methods were assessed using the environmental assessment tools of the analytical procedure: the Analytical Eco-Scale, Green Analytical Procedure Index (GAPI), and Analytical Greenness for Sample Preparation (AGREEprep). The method based on direct milk methylation received the highest scores. Omitting the lipid separation step has an impact on reducing the quantity of used toxic chemicals and reagents, and produces a smaller amount of waste, a much higher throughput, and a reduced cost analysis.
    Keywords:  environmental assessment tools; fatty acids; gas chromatography; greenness; milk fat
  22. Molecules. 2022 Nov 24. pii: 8195. [Epub ahead of print]27(23):
      A new analytical method for the determination of six volatile short and medium-chain fatty acids (acetic, propionic, isobutyric, isovaleric, hexanoic, and octanoic acids) through liquid-liquid extraction with diethyl ether, followed by GC-FID analysis, was developed and validated. The extraction conditions were optimized by evaluating the effect of the number of extractions (1 to 3) and the effect of the addition of salts (NaH2PO4, (NH4)2SO4, NaCl, (NH4)2SO4/NaH2PO4) to increase the concentration of the analytes in the ethyl ether phase. Results showed that a single extraction allows obtaining the highest sensitivity (due to the impossibility of evaporating the solvent to avoid losses of the analytes). The use of salting out agents, in particular, NaH2PO4, showed an important increase in the extraction extent, on average, 1.5 times higher as compared to the extraction performed without salt. The proposed method is rapid, requiring a total of 30 min for preparation and analysis, and it makes use of small amounts of sample (500 µL) and solvent (400 µL). The method was then applied to quantify the analytes in 5 white wines and 5 red wines, allowing to highlight some clear differences between red and white wines, with the red ones having a significantly higher amount of acetic acid (715.7 ± 142.3 mg/L in red wines and 351.5 ± 21.2 mg/L in white wines) and the white wines having a significantly higher amount of hexanoic and octanoic acid (6.1 ± 3.0 mg/L and 2.6 ± 0.8 mg/L, respectively, are the mean concentrations in white wines, and 4.7 ± 0.8 and 2.4 ± 0.4 mg/L, respectively, are the mean concentrations in red wines).
    Keywords:  flavor; gas chromatography; medium chain fatty acids (MCFAs); short chain fatty acids (SCFAs); volatile compounds; wine
  23. Int J Mol Sci. 2022 Nov 29. pii: 14960. [Epub ahead of print]23(23):
      The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with mixed hydrophobic/hydrophilic properties (cholesterol and alkylamide) were firstly used for this purpose with reversed-phased high-performance liquid chromatography. Several different chromatographic parameters were tested for their impact on impurities separation: type, concentration, pH of salt, as well as organic solvent type in the mobile phase. The pH was the most influential factor on the separation and signal intensities in mass spectrometry detection. Finally, the optimized method included the application of cholesterol stationary phase, with mobile phase containing 20 mM ammonium formate (pH 6.5) and methanol. It allowed good separation and the identification of most impurities within 25 min. Since not all closely related impurities could be fully resolved from the main peak in this oligonucleotide impurity profiling, two-dimensional liquid chromatography was used for peak purity determination of the target oligonucleotides. The Ethylene Bridged Hybrid (BEH) Amide column in hydrophilic interaction liquid chromatography was applied in the second dimension, allowing additional separation of three closely related impurities.
    Keywords:  impurities; mass spectrometry; oligonucleotide; separation; stationary phase; two-dimensional liquid chromatography
  24. Molecules. 2022 Nov 28. pii: 8306. [Epub ahead of print]27(23):
      In the pharmaceutical field, and more precisely in quality control laboratories, robust liquid chromatographic methods are needed to separate and analyze mixtures of compounds. The development of such chromatographic methods for new mixtures can result in a long and tedious process even while using the design of experiments methodology. However, developments could be accelerated with the help of in silico screening. In this work, the usefulness of a strategy combining response surface methodology (RSM) followed by multicriteria decision analysis (MCDA) applied to predictions from a quantitative structure-retention relationship (QSRR) model is demonstrated. The developed strategy shows that selecting equations for the retention time prediction models based on the pKa of the compound allows flexibility in the models. The MCDA developed is shown to help to make decisions on different criteria while being robust to the user's decision on the weights for each criterion. This strategy is proposed for the screening phase of the method lifecycle. The strategy offers the possibility to the user to select chromatographic conditions based on multiple criteria without being too sensitive to the importance given to them. The conditions with the highest desirability are defined as the starting point for further optimization steps.
    Keywords:  method development; multi-criteria decision analysis; response surface methodology; reversed-phase liquid chromatography; small pharmaceutical compounds
  25. Mol Omics. 2022 Dec 16.
      Metabolomics is the field of omics research that offers valuable insights into the complex composition of biological samples. It has found wide application in clinical diagnostics, disease investigation, therapy prediction, monitoring of treatment efficiency, drug discovery, or in-depth analysis of sample composition. A suitable study design constitutes the fundamental requirements to ensure robust and reliable results from the study data. The study design process should include a careful selection of conditions for each experimental step, from sample collection to data analysis. The pre-analytical variability that can introduce bias to the subsequent analytical process, decrease the outcome reliability, and confuse the final results of the metabolomics research, should also be considered. Herein, we provide key information regarding the pre-analytical variables affecting the metabolomics studies of biological fluids that are the most desirable type of biological samples. Our work offers a practical review that can serve and guide metabolomics pre-analytical design. It indicates pre-analytical factors, which can introduce artificial data variation and should be identified and understood during experimental design (through literature overview or analytical experiments).
  26. Anal Biochem. 2022 Dec 12. pii: S0003-2697(22)00478-X. [Epub ahead of print]662 115018
      Mass spectrometry imaging (MSI) is a powerful technique enabling the visualization of the spatial distribution of different molecules in tissue biopsies with different pathologies. Sample handling and preparing adipose tissue for MSI is challenging and prone to molecular delocalization due to tissue melting. In this work, we developed a method for matrix-assisted laser desorption/ionization (MALDI)-MSI to study lipids in human infrapatellar fat pad (IPFP), a biomarker source in musculoskeletal pathologies, while preserving molecular spatial distribution. Cryosectioning at 15 μm with a temperature below -30 °C, thaw-mounting, and sublimation, was demonstrated to preserve IPFP's heterogeneous appearance and spatial distribution of lipids.
    Keywords:  Adipose tissue; Delocalization; Hoffa's fat pad; Lipidomics
  27. Anal Chem. 2022 Dec 14.
      Untargeted mass spectrometry (MS) metabolomics is an increasingly popular approach for characterizing complex mixtures. Recent studies have highlighted the impact of data preprocessing for determining the quality of metabolomics data analysis. The first step in data processing with untargeted metabolomics requires that signal thresholds be selected for which features (detected ions) are included in the dataset. Analysts face the challenge of knowing where to set these thresholds; setting them too high could mean missing relevant features, but setting them too low could result in a complex and unwieldy dataset. This study compared data interpretation for an example metabolomics dataset when intensity thresholds were set at a range of feature heights. The main observations were that low signal thresholds (1) improved the limit of detection, (2) increased the number of features detected with an associated isotope pattern and/or an MS-MS fragmentation spectrum, and (3) increased the number of in-source clusters and fragments detected for known analytes of interest. When the settings of parameters differing in intensities were applied on a set of 39 samples to discriminate the samples through principal component analyses (PCA), similar results were obtained with both low- and high-intensity thresholds. We conclude that the most information-rich datasets can be obtained by setting low-intensity thresholds. However, in the cases where only a qualitative comparison of samples with PCA is to be performed, it may be sufficient to set high thresholds and thereby reduce the complexity of the data processing and amount of computational time required.
  28. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Oct 17. pii: S1570-0232(22)00404-4. [Epub ahead of print]1214 123499
      A sensitive and reliable method was developed to determine befotertinib (D-0316) and its metabolite D-0865 from human plasma by LC-MS/MS. The samples were prepared by simple protein precipitation and 2 µL of the supernatant were chromatographed on a C18 analytical column (ACE Excel 2 Super C18, 50 × 2.1 mm). Elution was performed with mobile phase A (10 mM ammonium acetate in water containing 1 % formic acid) and mobile phase B (acetonitrile containing 1 % formic acid) under a gradient program in a total run time of 4 min. Triple Quadruple 5500 equipped with Turbo Ion Spray source and multiple reaction monitoring (MRM) were used for the analysis detection. The transitions were m/z 568.3 → 72.1 m/z (befotertinib), m/z 554.2 → 497.2 (D-0865), and m/z 455.2 → 164.9 (verapamil, internal standard). According to the Chinese Pharmacopeia Commission and ICH Harmonised Guideline for Bioanalytical Method Validation, this method was validated within the spectrum of its accuracy, precision, selectivity, linearity, recovery, matrix effect, and stability. This LC-MS/MS method was successfully applied for the quantitation of befotertinib and its metabolite D-0865 in human plasma during the pharmacokinetics study of befotertinib in non-small cell lung cancer (NSCLC) patients.
    Keywords:  Befotertinib; LC-MS/MS; MRM; Metabolite D-0865; Method validation; Pharmacokinetics
  29. J Am Soc Mass Spectrom. 2022 Dec 12.
      We developed a structural identification method for eicosanoids with various ring structures using mass spectrometry. We discovered that an electron beam with a kinetic energy of 10 eV, which is in the Electron Impact Excitation of Ions from Organics (EIEIO) regime, cleaved the fatty acids enough to distinguish constitutional and cis/trans isomers. In addition to EIEIO, a comparison to authentic standards using differential mobility spectrometry (DMS) can identify diastereomers, which was difficult by EIEIO. The combination of EIEIO and DMS can provide a high-throughput method to identify complete structures of eicosanoids in mixed samples, which is not allowed with conventional analytical methods though eicosanoids are important signaling molecules in biosystems.