High-throughput Liquid Chromatography Research Articles

Simultaneous determination of tramadol and paracetamol in human plasma using LC-MS/MS and application in bioequivalence study of ­fixed-dose combination

The study aimed to develop a sensitive and high-throughput liquid chromatography coupled with tandem mass spectrometry method to quantify concentrations of tramadol and paracetamol simultaneously in human plasma. Sample preparation involved single-step protein precipitation using methanol and two deuterated internal standards, tramadol D6 and paracetamol D4. Agilent Poroshell 120 EC-C18 (100 × 2.1 mm, 2.1 µm) analytical column was employed to achieve chromatographic separation. Detection was in positive ion multiple reaction monitoring mode. A tailing factor (Tf) of <1.2, separation factor (K prime) of >1.5 from the column dead time and signal-to-noise (S/N) ratio >10, were obtained for analytes and internal standards. The standard curve was linear over the concentration range of 2.5–500.00 ng/mL for tramadol and 0.025–20.00 μg/mL for paracetamol. A small injection volume of 1 µL, low flow rate of 440 µL/min and short analysis time of 3.5 min reduced the solvent consumption, analysis cost and system contamination. The results of method validation parameters fulfilled the acceptance criteria of bioanalytical guidelines. The method was successfully applied to a bioequivalence study of fixed-dose combination products of tramadol and paracetamol in Malaysian healthy subjects.

An integrated approach to evaluate acetamiprid-induced oxidative damage to tRNA in human cells based on oxidized nucleotide and tRNA profiling

Acetamiprid is poisonous to mammals due to severe acetamiprid-induced oxidative stress that could cause mitochondrial dysfunctions, lipid and protein oxidation, inflammation, apoptosis, and DNA damage. Evidence has accumulated for the role of oxidative stress in changing structures and functions of transfer RNAs (tRNAs) by inducing tRNA cleavage, reprogramming tRNA modifications and impairing aminoacyl-tRNA synthetase editing sites. However, the impact of acetamiprid-induced oxidative stress on tRNA is still unknown. Here, we investigated the effects of acetamiprid on cell viability, reactive oxygen species (ROS) levels, DNA damage, cellular oxidized nucleotide concentrations, and oxidative damage to tRNA in HepG2 cells and LO2 cells. Acetamiprid can cause the significant increment of ROS and DNA oxidative damage. In this study, an integrated approach was established to simultaneously study the network of oxidized nucleotides and explore the tRNA oxidative damage after acetamiprid exposure. A simple and high-throughput liquid chromatography with tandem mass spectrometry (LC-MS/MS) method coupled with (trimethylsilyl)diazomethane (TMSD) derivatization was successfully developed to quantify 12 cellular oxidized nucleotides that cannot be detected using traditional detection methods because of the huge interferences from naturally abundant nucleotides. Meanwhile, the accumulation rate and the locating sites of 8-oxo-2, 7-dihydro-guanine (8-oxo-G) in tRNA were inspected using the established N-(tert-Butyldimethylsilyl)-N-methyl-trifluoroacetamide (MTBSTFA) labeling-based tRNA profiling method. After acetamiprid treatment, the increment of oxidized nucleoside triphosphates is smaller than that of their corresponding mono- and diphosphates, as well as the dephosphorylated nucleosides, on account of the existence of sanitization enzymes. Several tRNA fragments, CUC[m1A]Gp, CACGp, [Cm]C[m2G]p, and DDGp, are significantly downregulated in acetamiprid-treated HepG2 cells, while only [Cm]C[m2G]p in acetamiprid-treated LO2 cells. According to the profiling results, the significantly changed fragment CUC[m1A]Gp might be caused by the oxidation of guanine (G) to form 8-oxo-G at position 15 in human tRNAphe([Gm]AA), providing more information about the effect of oxidized nucleobases on tRNA’s functions.

Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses

Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative accuracy, and provide opportunities for more decisive troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of N = 335 patient samples using tandem mass tag (TMTpro) 16-plex batches. Over the course of a 10-month data acquisition period for this cohort we collected 271 pooled QC LC-MS/MS result files obtained from MS/MS analysis of a patient-derived pooled plasma sample, representative of the entire cohort population. This sample was tagged with TMTzero or TMTpro reagents and used to inform the daily performance of the LC-MS/MS instruments and to allow within and across sample batch normalization. Analytical variability of a number of instrumental and data analysis metrics including protein and peptide identifications, peptide spectral matches (PSMs), number of obtained MS/MS spectra, average peptide abundance, percent of peptides with a Δ m/z between ±0.003 Da, percent of MS/MS spectra obtained at the maximum injection time, and the retention time of selected tracking peptides were evaluated to help inform the design of a robust LC-MS/MS QC workflow for use in future cohort studies. This study also led to general tips for using selected metrics to inform real-time troubleshooting of LC-MS/MS performance issues with daily QC checks.

Abstract P203: Healthy Lifestyle Plasma Metabolite Profile and Risk of Mortality in US Prospective Cohort Studies

Background: A healthy lifestyle is associated with a lower risk of premature death. Metabolic pathways of a healthy lifestyle and their association with mortality remain to be understood. This study aimed to identify the metabolomic profile of a healthy lifestyle score and examine its prospective association with all-cause and cause-specific mortality, including death from cardiovascular disease (CVD) and cancer. Methods: The population included 12,146 participants from the Nurses’ Health Study (NHS), NHS II and Health Professionals Follow-Up Study (HPFS)(83% women, 97% white, aged 55±9y). Plasma metabolites were profiled using high-throughput liquid chromatography mass-spectrometry at baseline (NHS:1989-1990; NHSII:1996-1999; HPFS:1993-1995). The healthy lifestyle score was computed by summing the total number of healthy lifestyle factors participants adhered to from validated questionnaires at baseline: healthy diet (Alternative Healthy Eating Index, upper 40%), moderate alcohol intake (women: 5-15 g/d; men: 5-30 g/d), moderate-to-vigorous physical activity (≥30min/d), never smoking and normal BMI (18.5-24.9kg/m 2 ). Deaths were ascertained with death certificates and medical records. The metabolite profile was identified using elastic net regressions with train test validation split (70-30%). Metabolic pathways were determined using Metabolite Set Enrichment Analysis (MSEA). Multivariable-adjusted Cox proportional hazards regressions were used to estimate hazard ratios and 95% confidence intervals (HR[CI]) per unit of score of the healthy lifestyle metabolite profile with mortality risk. Results: The identified profile included 88 metabolites and correlated with the healthy lifestyle score (Pearson r=0.43-0.44; p&lt;0.001). Triglyceride and diglyceride metabolite sets were inversely associated with the healthy lifestyle score, whereas cholesteryl ester and phosphatidylcholine plasmalogen sets were directly associated (p&lt;0.001). Among individual lifestyle factors, the profile was most strongly correlated with normal BMI (r pb =0.43; p&lt;0.001). Over 32y of follow-up, there were 3,851 deaths, including 749 deaths from CVD and 994 from cancer. Participants with a higher healthy lifestyle metabolite profile score had lower risk of all-cause (HR=0.79[0.73, 0.85]) and CVD mortality (HR=0.77[0.58, 0.95]), but not cancer (HR=0.91[0.77, 1.05]). Significant associations persisted after further adjustment for the healthy lifestyle score. Conclusions: In US adults, we identified a metabolite profile related to a healthy lifestyle largely reflecting lipid metabolism pathways. A higher metabolite score was associated with lower subsequent all-cause mortality risk, specifically from CVD. Findings provide novel insights into potential metabolic pathways underlying the association between a healthy lifestyle and lower premature mortality.

Metabolite Signature of Simvastatin Treatment Involves Multiple Metabolic Pathways.

Statins inhibit the 3-hydroxy-3-methylglutaryl-CoA reductase enzyme and are the most widely used medication for hypercholesterolemia. Previous studies on the metabolite signature of simvastatin treatment have included only a small number of metabolites. We performed a high-throughput liquid chromatography–tandem mass spectroscopy profiling on the effects of simvastatin treatment on 1098 metabolite concentrations in the participants of the METSIM (Metabolic Syndrome In Men) study including 1332 participants with simvastatin treatment and 6200 participants without statin treatment. We found that simvastatin exerts profound pleiotropic effects on different metabolite pathways, affecting not only lipids, but also amino acids, peptides, nucleotides, carbohydrates, co-factors, vitamins, and xenobiotics. We identified 321 metabolites significantly associated with simvastatin treatment, and 313 of these metabolites were novel. Our study is the first comprehensive evaluation of the metabolic signature of simvastatin treatment in a large population-based study.

LC-MS/MS-MS3 for determination and quantification of Δ9-tetrahydrocannabinol and metabolites in blood samples

Due to the high prevalence of cannabinoids in forensic toxicology, it is crucial to have an efficient method that allows the use of a small sample amount and that requires a minimal sample preparation, for the determination and quantification of low concentrations. A simple, highly selective and high throughput liquid chromatography tandem mass spectrometry method (LC-MS/MS-MS3) was developed for the determination and quantification of Δ9-tetrahydrocannabinol (THC), 11-hydroxy-Δ9-THC (THC-OH) and 11-nor-Δ9-THC-9-carboxylic acid (THC-COOH) in blood samples. Chromatographic analysis was preceded by a protein precipitation of 0.1 mL of blood samples with acetonitrile, then THC, THC-OH, THC-COOH and deuterated internal standards were separated on an Acquity UPLC® HSS T3 (100 mm × 2.1 mm i.d., 1.8 mm) reversed-phase column using a gradient elution with 2 mM aqueous ammonium formate (0.1% formic acid) and methanol, at a flow rate of 0.4 mL/min, and with a run time of 10 min. For MS/MS-MS3 analysis, a SCIEX QTRAP® 6500+ linear ion trap triple quadrupole mass spectrometer was used via electrospray ionization (ESI), operated in multiple reaction mode (MRM) and linear ion trap mode (MS3). The method was validated in accordance with international accepted criteria and guidelines. The method was selective and linear between 0.5–100 ng/mL (r2 > 0.995). The lower limits of quantification (LLOQ) corresponded to the lowest concentrations used for the calibration curves. The coefficients of variation obtained for accuracy and precision were less than 15%. The mean recoveries were between 88.0–101.4% for the studied concentration levels (1 ng/mL, 5 ng/mL and 50 ng/mL). No significant interfering compounds, matrix effects or carryover were observed. The validated method provides a sensitive, efficient and robust procedure for the quantitation of cannabinoids in blood using LC–MS/MS-MS3 and a sample volume of 0.1 mL. This work is also a proof of concept for using LC-MS3 technique to determine drugs in biological samples.

Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform.

Single-cell proteomics (SCP) has great potential to advance biomedical research and personalized medicine. The sensitivity of such measurements increases with low-flow separations (<100 nL/min) due to improved ionization efficiency, but the time required for sample loading, column washing, and regeneration in these systems can lead to low measurement throughput and inefficient utilization of the mass spectrometer. Herein, we developed a two-column liquid chromatography (LC) system that dramatically increases the throughput of label-free SCP using two parallel subsystems to multiplex sample loading, online desalting, analysis, and column regeneration. The integration of MS1-based feature matching increased proteome coverage when short LC gradients were used. The high-throughput LC system was reproducible between the columns, with a 4% difference in median peptide abundance and a median CV of 18% across 100 replicate analyses of a single-cell-sized peptide standard. An average of 621, 774, 952, and 1622 protein groups were identified with total analysis times of 7, 10, 15, and 30 min, corresponding to a measurement throughput of 206, 144, 96, and 48 samples per day, respectively. When applied to single HeLa cells, we identified nearly 1000 protein groups per cell using 30 min cycles and 660 protein groups per cell for 15 min cycles. We explored the possibility of measuring cancer therapeutic targets with a pilot study comparing the K562 and Jurkat leukemia cell lines. This work demonstrates the feasibility of high-throughput label-free single-cell proteomics.

Simultaneous determination of clopidogrel, 2-oxo-clopidogrel, and the thiol metabolite of clopidogrel in human plasma by LC-MS/MS.

Clopidogrel is a pro-drug which needs two-step metabolism to produce the active thiol metabolite. This study aimed to explore an efficient method to simultaneously determine the plasma clopidogrel, 2-oxo-clopidogrel (2-Oxo-CLP), and the clopidogrel active metabolite (CAM). A high-throughput liquid chromatography tandem mass spectrometry (LC-MS/MS) was therefore developed. The analytes were extracted from plasma by using methyl tert-butyl ether (MTBE). Chromatographic separation was performed on a C18 column under an isocratic elution, accompanied with acetonitrile and deionized water containing 0.1% formic acid. After optimizing the condition of LC-MS/MS, a stable linearity was observed in the standard curves over the concentration ranges of 0.05 to 50.0 ng/mL for clopidogrel, 0.5 to 50.0 ng/mL for 2-Oxo-CLP, and 0.5 to 100 ng/mL for clopidogrel active metabolite derivative (CAMD). The retention time was 4.78 minutes, 3.79 minutes, 3.59 minutes, and 4.82 minutes for clopidogrel, 2-Oxo-CLP, CAMD, and internal standard, respectively. Both the relative standard deviation and the relative error were within the requirement of operating criteria. No significant degradation of clopidogrel, 2-Oxo-CLP, and CAMD occurred under different storage conditions. This method was successfully validated in 3 patients with coronary artery disease. The results showed that the current LC-MS/MS method was efficient for simultaneously detecting clopidogrel, 2-Oxo-CLP, and CAM with fine linearity, accuracy, precision, and stability.

Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

BackgroundBupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway.ResultsTranscript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families.ConclusionsOur results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.

A novel high-throughput liquid chromatography assay for Carbohydrate-Deficient transferrin (CDT) based on flow-modulated isocratic elution and terbium-induced fluorescence

Transferrin is a glycoprotein containing two bi- or tri-antennary carbohydrate chains ending with sialic acid. Its glycosylation is reduced in chronic alcohol abuse and in inborn glycosylation pathologies, where the carbohydrate-deficient fraction of the protein (CDT) increases significantly. The current methods require a gradient chromatographic separation and time-consuming sample preparation. In comparison, the proposed approach uses a novel flow-modulated liquid chromatography technique (fmLC) and a highly selective and sensitive fluorescence derivatization reaction with terbium ion.A fmLC-FLD method using isocratic anion exchange separation was optimized and validated to resolve disialo-transferrin and trisialo-transferrin from other transferrin glycoforms. Detection took place by recording fluorescence at 550 nm wavelength (excitation at 298 nm). The chromatographic separation needed 5 min, allowing seriate injection every 7.5 min.The method was validated according to the current guidelines of analytical chemistry showing adequate accuracy and precision for the quantitative determination of CDT. The proposed method proved also to be suitable to analyse haemolyzed sera which, because of interference by haemoglobin, fail the standard HPLC-Vis analysis. The method was tested in parallel with HPLC-Vis on 131 sera showing an excellent correlation of results proved by a correlation coefficient of 0.995 (Pearson’s r).The proposed approach proved much simpler than the current methods and cheaper in terms of instrumental costs offering a ground-breaking analytical tool that could likely make available the characterization of CDT outside specialized laboratories, such as in occupational medicine centres, doctor’s offices, small laboratories, alcohol rehabilitation centres, and in developing countries.

Comparison of LC–MS3 and LC–MRM strategy for quantification of methotrexate in human plasma and its application in therapeutic drug monitoring

A simple, highly selective and high throughput liquid chromatography tandem mass spectrometry cubed (LC/MS3) method was developed and validated for quantification of methotrexate in human plasma. The MS3 detection is a scanning mode of QTrap MS systems or ion trap MS systems. After simple protein precipitation with methanol, methotrexate and methotrexate-d3 were separated on an Agilent Poroshell 120 SB-C18 column (4.6 × 50 mm, 2.7 µm) using isocratic elution with a mobile phase consisting of 60% 0.1% formic acid in water and 40% 0.1% formic acid in acetonitrile. The flow rate is 0.8 mL/min. MS3 detection in positive ion mode used the MRM3 transitions at m/z 455.2→308.2→175.1 for quantification of methotrexate and m/z 458.2→311.2→175.1 for quantification of methotrexate-d3. The total run time was only 3 min for each sample. The LC/MS3 assay was linear in the concentration range 10–3000 ng/mL(R2 ≥ 0.995) and the intra- and inter-day accuracies were< 3.72% and precisions were< 7.78% at all concentrations. The absolute recoveries (%) and matrix effect (%) for methotrexate in human plasma were between 92.6 and 114.3. The novelty of the presented methodology is the MS3 technique resulting in enhanced selectivity and sensitivity. The application of this LC-MS3 method was successfully completed on 46 human plasma samples and the quantitative results of identical human plasma samples were compared with another LC-MRM based method. Passing–Bablok regression coefficients demonstrated that there is no significant difference between the LC-MS3 method and LC-MRM method. Bland–Altman plots showed a concordant results, supporting the developed LC–MS3 method is a reliable and accurate assay for determination of methotrexate in human plasma. This work is also a proof of concept for using LC-MS3 technique to determination of chemicals in biological samples.

Metabolic Biomarkers of Mediterranean Diet in Pregnant Women

Abstract Objectives Using an untargeted approach to identify plasma metabolomics signature of the Mediterranean diet, a healthful dietary pattern related to both maternal and fetal outcomes, in pregnancy. Methods This study included 193 pregnant women from the NICHD Fetal Growth Studies-Singletons (FGS) cohort who had habitual dietary intake in the past three months measured at 8–13 gestational weeks (GW) by the semi-quantified food frequency questionnaire. Fasting plasma metabolomics profiles at 15–26 GW were measured by the high-throughput liquid chromatography quadrupole time of-flight mass spectrometry (LC-QTOF MS/MS). Metabolites were re-scaled to a median of 1 for each batch and log transformed. Alternate Mediterranean Diet (aMED) score was calculated by eight food and nutrient components (i.e., fruits, vegetables, whole grains, nuts, fish, legumes, red and processed meats, and monounsaturated-to-saturated fat ratio), with a higher score indicating a better adherence. Prospective associations of aMED score in peri-conception and early pregnancy with individual metabolites at 15–26 GW were estimated using the linear regression adjusting for potential confounders and multiple testing. LASSO (Least Absolute Shrinkage and Selection Operator) regression with 10-fold cross-validation was performed to select metabolites that were jointly associated with high aMED score (defined as the top tertile). All statistical analyses were weighted to represent the entire FGS cohort. Results A total of 460 known metabolites were profiled and annotated. Six metabolites were selected as the biomarkers of high aMED score by the LASSO regression (i.e., with no-zero coefficients). Among them, glutamic acid and 3-hydroxybutyric acid were negatively whereas PC (40:7), CE (20:5), TG (49:1), and TG (58:4) were positively associated with aMED score. The six biomarkers were also confirmed by the linear regression with false discovery rates &amp;lt; 0.1. Conclusions Our study is the first one conducted in pregnant women using the untargeted metabolomics approach and we newly identified several biomarkers of Mediterranean diet in pregnant women. Results from this study warrant the replication by future studies. Funding Sources The work was supported by the intramural research program of the NICHD and the internal fund from UCLA.

Putting Proteomics Into Immunotherapy for Glioblastoma.

In glioblastoma, the most aggressive brain cancer, a complex microenvironment of heterogeneity and immunosuppression, are considerable hurdles to classify the subtypes and promote treatment progression. Treatments for glioblastoma are similar to standard therapies for many other cancers and do not effectively prolong the survival of patients, due to the unique location and heterogeneous characteristics of glioblastoma. Immunotherapy has shown a promising effect for many other tumors, but its application for glioma still has some challenges. The recent breakthrough of high-throughput liquid chromatography–mass spectrometry (LC-MS/MS) systems has allowed researchers to update their strategy for identifying and quantifying thousands of proteins in a much shorter time with lesser effort. The protein maps can contribute to generating a complete map of regulatory systems to elucidate tumor mechanisms. In particular, newly developed unicellular proteomics could be used to determine the microenvironment and heterogeneity. In addition, a large scale of differentiated proteins provides more ways to precisely classify tumor subtypes and construct a larger library for biomarkers and biotargets, especially for immunotherapy. A series of advanced proteomic studies have been devoted to the different aspects of immunotherapy for glioma, including monoclonal antibodies, oncolytic viruses, dendritic cell (DC) vaccines, and chimeric antigen receptor (CAR) T cells. Thus, the application of proteomics in immunotherapy may accelerate research on the treatment of glioblastoma. In this review, we evaluate the frontline applications of proteomics strategies for immunotherapy in glioblastoma research.

High-Throughput Microbore Ultrahigh-Performance Liquid Chromatography-Ion Mobility-Enabled-Mass Spectrometry-Based Proteomics Methodology for the Exploratory Analysis of Serum Samples from Large Cohort Studies.

The deployment of proteomic analysis in clinical studies represents a significant opportunity to detect and validate biomarkers in translational medicine, improve disease understanding, and provide baseline information on population health. However, comprehensive proteome studies usually employ nanoscale chromatography and often require several hours of analysis/sample. Here, we describe a high-throughput liquid chromatography tandem mass spectrometry (LC/MS/MS) methodology using 1 mm scale chromatography requiring only 15 min/sample, coupled to ion mobility-enabled mass spectrometry. The short run time effected a 6-fold increase in productivity compared with nanoscale LC/MS. The method demonstrated excellent reproducibility with retention time coefficient of variations of less than 0.05% and peak area reproducibility ranging from 5 to 15%. The 1 mm system produced similar chromatographic peak capacity values to the nanoscale miniaturized system, detecting 90% of the Escherichia coli proteins identified by the 75 μm LC/MS system (albeit based on only 75% of the peptides found by the latter). Application to the analysis of serum samples from a human prostate cancer study group resulted in the identification of a total of 533 proteins revealing the differential expression of proteins linked to patients receiving hormone-radiotherapy or undergoing surgery.

Secretome Analysis of Inductive Signals for BM-MSC Transdifferentiation into Salivary Gland Progenitors.

Severe dry mouth in patients with Sjögren’s Syndrome, or radiation therapy for patients with head and neck cancer, significantly compromises their oral health and quality of life. The current clinical management of xerostomia is limited to palliative care as there are no clinically-proven treatments available. Previously, our studies demonstrated that mouse bone marrow-derived mesenchymal stem cells (mMSCs) can differentiate into salivary progenitors when co-cultured with primary salivary epithelial cells. Transcription factors that were upregulated in co-cultured mMSCs were identified concomitantly with morphological changes and the expression of acinar cell markers, such as α-amylase (AMY1), muscarinic-type-3-receptor(M3R), aquaporin-5(AQP5), and a ductal cell marker known as cytokeratin 19(CK19). In the present study, we further explored inductive molecules in the conditioned media that led to mMSC reprogramming by high-throughput liquid chromatography with tandem mass spectrometry and systems biology. Our approach identified ten differentially expressed proteins based on their putative roles in salivary gland embryogenesis and development. Additionally, systems biology analysis revealed six candidate proteins, namely insulin-like growth factor binding protein-7 (IGFBP7), cysteine-rich, angiogenetic inducer, 61(CYR61), agrin(AGRN), laminin, beta 2 (LAMB2), follistatin-like 1(FSTL1), and fibronectin 1(FN1), for their potential contribution to mMSC transdifferentiation during co-culture. To our knowledge, our study is the first in the field to identify soluble inductive molecules that drive mMSC into salivary progenitors, which crosses lineage boundaries.

Proteomics and phosphoproteomics revealed molecular networks of stomatal immune responses.

Dynamic protein and phosphoprotein profiles uncovered the overall regulation of stomata movement against pathogen invasion and phosphorylation states of proteins involved in ABA, SA, calcium and ROS signaling, which may modulate the stomatal immune response. Stomatal openings represent a major route of pathogen entry into the plant, and plants have evolved mechanisms to regulate stomatal aperture as innate immune response against bacterial invasion. However, the mechanisms underlying stomatal immunity are not fully understood. Taking advantage of high-throughput liquid chromatography mass spectrometry (LC-MS), we performed label-free proteomic and phosphoproteomic analyses of enriched guard cells in response to a bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. In total, 495 proteins and 1229 phosphoproteins were identified as differentially regulated. These proteins are involved in a variety of signaling pathways, including abscisic acid and salicylic acid hormone signaling, calcium and reactive oxygen species signaling. We also showed that dynamic changes of phosphoprotein WRKY transcription factors may play a crucial role in regulating stomata movement in plant immunity. The identified proteins/phosphoproteins and the pathways form interactive molecular networks to regulate stomatal immunity. This study has provided new insights into the multifaceted mechanisms of stomatal immunity. The differential proteins and phosphoproteins are potential targets for engineering or breeding of crops for enhanced pathogen defense.

A high throughput approach for determination of dermorphin in human urine using liquid chromatography-mass spectrometry for doping control purposes.

Dermorphin is a peptide with analgesic actions similar to morphine, but with greater effect and less potential to cause tolerance. The use of dermorphin has been documented in race horses, and its use in humans has already been reported. Considering the potential advantages from the use of dermorphin over morphine, a method to monitor it, and its main metabolite dermorphin (1-4) in humans becomes necessary for doping control. Here, we present two orthogonal methods for this purpose: a high-throughput liquid chromatography coupled to high-resolution mass spectrometry (HRMS) as an initial testing procedure and liquid chromatography-tandem mass spectrometry (MS/MS) in the selected reaction monitoring (SRM) acquisition mode for a confirmation procedure. For urine samples, pretreatment through a mixed-mode weak cation-exchange solid-phase extraction emerged as an effective approach to extract peptides from the biological sample. For the HRMS analysis, a full-MS scan acquisition mode was selected to detect the exact masses of dermorphin and dermorphin (1-4) at m/z 803.37226 and 457.20816, respectively. The SRM method used in the MS/MS confirmation protocol presented high specificity and sensitivity. The selected product ions for dermorphin were 602.2, 202.1 and 574.3 and for dermorphin (1-4) were 207.1, 223.1, and 235.1. Both methods were evaluated for specificity, repeatability, carryover, matrix effects, and recovery. No carryover and matrix effects were detected. The limit of detection for initial testing procedure and the limit of identification for confirmation procedure was 2.5 ng/ml. Also, specificity and robustness were acceptable for the application. Together, the developed methods proved to be efficient for the analysis of dermorphin and metabolite for human doping control purpose.

High-Throughput Liquid Chromatography-Tandem Mass Spectrometry Quantification of Glycosaminoglycans as Biomarkers of Mucopolysaccharidosis II.

We recently developed a blood–brain barrier (BBB)-penetrating enzyme transport vehicle (ETV) fused to the lysosomal enzyme iduronate 2-sulfatase (ETV:IDS) and demonstrated its ability to reduce glycosaminoglycan (GAG) accumulation in the brains of a mouse model of mucopolysaccharidosis (MPS) II. To accurately quantify GAGs, we developed a plate-based high-throughput enzymatic digestion assay coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS) to simultaneously measure heparan sulfate and dermatan sulfate derived disaccharides in tissue, cerebrospinal fluid (CSF) and individual cell populations isolated from mouse brain. The method offers ultra-high sensitivity enabling quantitation of specific GAG species in as low as 100,000 isolated neurons and a low volume of CSF. With an LOD at 3 ng/mL and LLOQs at 5–10 ng/mL, this method is at least five times more sensitive than previously reported approaches. Our analysis demonstrated that the accumulation of CSF and brain GAGs are in good correlation, supporting the potential use of CSF GAGs as a surrogate biomarker for brain GAGs. The bioanalytical method was qualified through the generation of standard curves in matrix for preclinical studies of CSF, demonstrating the feasibility of this assay for evaluating therapeutic effects of ETV:IDS in future studies and applications in a wide variety of MPS disorders.

Mass spectrometric quantification of urinary 6-sulfatoxymelatonin: age-dependent excretion and biological variation.

Regulators of circadian rhythm, including melatonin, influence fundamental biological processes. Measuring the melatonin metabolite 6-sulfatoxymelatonin in urine can estimate melatonin production. 6-sulfatoxymelatonin is mainly analyzed by immunoassays, but these methods are hampered by cross-reactivity and poor reproducibility when used to analyze small molecules. Therefore, we validated a high-throughput liquid chromatography with tandem mass spectrometry (LC-MS/MS) method to quantify 6-sulfatoxymelatonin in urine. We evaluated age-dependent 24-h excretion of 6-sulfatoxymelatonin into urine and the biological variation of urinary excretion in healthy individuals. The online solid phase extraction method combined with LC-MS/MS was validated according to international guidelines, and used to measure the excretion of 6-sulfatoxymelatonin into urine of 240 healthy individuals. Biological variation of 6-sulfatoxymelatonin excretion was examined in 10 healthy individuals. Urinary 6-sulfatoxymelatonin results were well within the validation criteria (interassay coefficient of variation:<5.4%, quantification limit: 0.2nmol/L). There was an age-related decrease in 6-sulfatoxymelatonin excretion into 24-h urine [F(5, 234)=13.9; p<0.001]. Within-subject variation of 6-sulfatoxymelatonin was 39.2% in day urine, 15.1% in night urine, and 12.2% in 24-h urine. Between-subject variation was 39.1% in day urine, 37.9% in night urine, and 36.8% in 24-h urine. This MS-based method enables straightforward, reproducible, and sensitive quantification of 6-sulfatoxymelatonin in urine. Urinary 6-sulfatoxymelatonin levels decreased with age. Biological variation of 6-sulfatoxymelatonin excretion into urine was high between subjects and lower within subjects, indicating that repeated measurements of 6-sulfatoxymelatonin in 24-h urine are needed in future studies.

Enrichment-free High-throughput Liquid Chromatography-Multiple-Reaction Monitoring Quantification of Cytochrome P450 Proteins in Plated Human Hepatocytes Direct from 96-Well Plates Enables Routine Protein Induction Measurements.

Despite the availability of liquid chromatography (LC)-mass spectrometry (MS) methods for quantifying cytochrome P450 (P450) proteins, incorporation of P450 protein quantification into induction study workflows has not been widely adopted. To more readily enable P450 protein quantification in induction study workflows, DMPK research groups need a simple, robust, cost-effective, high-throughput method compatible with 96-well-plated human hepatocyte formats. Here, we provide such a methodology. Our method bypasses both microsomal enrichment and antibody-based enrichment to go directly from the plate to LC-MS/MS analysis. We use this "plate-to-peaks" approach for quantifying CYP3A4, CYP2B6, and CYP1A2, the major inducible hepatic P450s representative of pregnane X receptor-, constitutive androstane receptor-, and aryl hydrocarbon receptor-mediated induction, respectively. We leveraged our induction study-aligned assay format to assess induction across mRNA, protein, and enzyme activity using known induction control compounds. As expected, results from the three methods using model inducers were broadly concordant, but the magnitude of the induction response differed. Induction of CYP3A4 using 10 µM rifampicin was 12-fold for RNA, eightfold for protein, and threefold for activity; for CYP1A2 with 50 µM omeprazole, induction was 30-fold for RNA, 13-fold for protein, and 17-fold for activity; for CYP2B6 with 50 µM phenytoin, induction was 23-fold for RNA, twofold for protein, and fivefold for activity. Most importantly, we anticipate the relative ease of this method will enable researchers to routinely adopt P450 protein quantification as part of nonclinical evaluation of P450 induction. SIGNIFICANCE STATEMENT: Current methodologies for quantifying P450 proteins by liquid chromatography (LC)-tandem mass spectrometry are either cumbersome, too costly, or both to be widely adopted into induction study workflows by the ADME research community. We present a simplified LC-MS/MS methodology for quantifying P450 proteins directly from human hepatocytes, without any form of enrichment, in 96-well induction assay plate format that should be readily adoptable by any ADME laboratory with LC-multiple-reaction monitoring capabilities.