MS Strategy Research Articles

Simultaneous Qualitative and Quantitative Analyses of 41 Constituents in Uvaria macrophylla Leaves Screen Antioxidant Quality-Markers Using Database-Affinity Ultra-High-Performance Liquid Chromatography with Quadrupole Orbitrap Tandem Mass Spectrometry.

To date, no study has focused on Uvaria macrophylla leaves with various traditional efficiencies. This paper therefore applied a database affinity ultra-high-performance liquid chromatography with quadrupole Orbitrap tandem mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) strategy to analyze the lyophilized aqueous extract of U. macrophylla leaves. Through database comparison and MS fragment elucidation, this study has putatively identified 41 constituents belonging to flavonoid, phenolic acid, steroid, and saccharide natural product classifications. Significantly, four groups of isomers (liquiritigenin vs. isoliquiritigenin vs. pinocembrin; oroxylin A vs. wogonin vs. galangin 3-methyl ether; isoquercitrin vs. hyperoside; protocatechuic acid vs. 2,5-dihydroxybenzoic acid) have been successfully distinguished from each other. All of 41 constituents were then subjected to a quantitative analysis based on linear regression equation established by the above UHPLC-Q-Orbitrap-MS/MS strategy and an ABTS+•-scavenging antioxidant assay. Finally, the chemical content was multiplied by the corresponding ABTS+•-scavenging percentage to calculate the antioxidant contribution. It was shown that the chemical contents of 41 constituents varied from 0.003 ± 0.000 to 14.418 ± 1.041 mg/g, and gallic acid showed the highest antioxidant contribution. Gallic acid is considered as a suitable antioxidant quality-marker (Q-marker) of U. macrophylla leaves. These findings have scientific implications for the resource development and quality control of U. macrophylla leaves.

Towards a universal method for middle-down analysis of antibodies via proton transfer charge reduction-Orbitrap mass spectrometry.

Modern mass spectrometry technology allows for extensive sequencing of the ~ 25kDa subunits of monoclonal antibodies (mAbs) produced by IdeS proteolysis followed by disulfide bond reduction, an approach known as middle-down mass spectrometry (MD MS). However, the spectral congestion of tandem mass spectra of large polypeptides dramatically complicates fragment ion assignment. Here, we report the development and benchmark of an MD MS strategy based on the combination of different ion fragmentation techniques with proton transfer charge reduction (PTCR) to simplify the gas-phase sequencing of mAb subunits. Applied on the liquid chromatography time scale using an Orbitrap Tribrid mass spectrometer, PTCR produces easy-to-interpret mass spectra with limited ion signal overlap. We demonstrate that the accurate estimation of the number of charges submitted to the Orbitrap mass analyzer after PTCR allows for the detection of charge-reduced product ions over a wide mass-over-charge (m/z) window with low parts per million m/z accuracy. Therefore, PTCR-based MD MS analysis increases not only sequence coverage, number of uniquely identified fragments, and number of assigned complementary ion pairs, but also the general confidence in the assignment of subunit fragments. This data acquisition method can be readily applied to any class of mAbs without an apparent need for optimization, and benefits from the high resolving power of the Orbitrap mass analyzer to return sequence coverage of individual subunits exceeding 80% in a single run, and > 90% when just two experiments are combined.

IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.

Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of predefined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (lrRNA-seq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNaseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This lrRNA-seq-informed Tomahto targeted approach is a new modality for generating protein-level evidence of alternative isoforms─a critical first step in designing functional studies and eventually clinical assays.

Automated sequential SPME addressing the displacement effect in food samples

The displacement effect can be an issue for the quantitation of analytes with low affinity towards the extraction phase in solid-phase microextraction (SPME) for food samples that have low level of binding matrix or high level of hydrophobic compounds. In this communication, automated sequential SPME-GC–MS strategy was developed for addressing the displacement issue. The SPME thin film with PDMS coating was firstly used for the extraction of hydrophobic components in the sample which cause displacement and then SPME fiber with DVB/CAR/PDMS coating was applied in the second step for the extraction of the remain compounds. This new strategy was investigated by using 10 key food odorants as target analytes and tested in commercial beer samples. The results suggested that sequential SPME can decrease the displacement effect and improve the extraction efficiency for polar analytes.

Dracorhodin targeting CMPK2 attenuates inflammation: A novel approach to sepsis therapy.

Despite all modern advances in medicine, an effective drug for treating sepsis has yet to be found. The discovery of CMPK2 spurred hopes for the treatment of sepsis. However, CMPK2-untapped target inhibitors are still an enormous obstacle that has hindered the CMPK2-centric treatment of sepsis. Here, we found that the CMPK2 gene is highly expressed in the whole blood of sepsis patients by RNA-Seq. First, recombinant CMPK2 was purified by a eukaryotic expression purification system, and the activity of recombinant CMPK2 was detected by the ADP-GLO assay. Second, we developed an affinity MS strategy combined with quantitative lysine reactivity profiling to discover CMPK2 ligands from the active ingredients of Chinese herbs. In addition, the dissociation constant Kd of the ligand and the target protein CMPK2 was further detected by microscale thermophoresis technology. Third, we used this strategy to identify a naturally sourced small molecule, dracorhodin (DP). Using mass spectrometry-based quantitative lysine reactivity profiling combined with a series of mutant tests, the results show that K265 acts as a bright hotspot of DP inhibition of CMPK2. Fourth, immune-histochemical staining, ELISAs, RT-qPCR, flow cytometry and immunoblotting were used to illustrate the potential function and related mechanism of DP in regulating sepsis injury. Our results suggest that DP exerts powerful anti-inflammatory effects by regulating the NLRP3 inflammasome via the lipopolysaccharide (LPS)-induced CMPK2 pathway. Strikingly, DP significantly attenuated LPS-induced sepsis in a mouse model, but its effect was weakened in mice with myeloid-specific Cmpk2 ablation. We provide a new framework that provides more valuable information for new therapeutic approaches to sepsis, including the establishment of screening strategies and the development of target drugs to provide a theoretical basis for ultimately improving clinical outcomes for sepsis patients. Collectively, these findings reveal that DP is a promising CMPK2 inhibitor for the treatment of sepsis.

Identification of Francisella tularensis Subspecies in a Clinical Setting Using MALDI-TOF MS: An In-House Francisella Library and Biomarkers.

Francisella tularensis is a zoonotic bacterium that is endemic in large parts of the world. It is absent in the standard library of the most applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems: the Vitek MS and the Bruker Biotyper system. The additional Bruker MALDI Biotyper Security library contains F. tularensis without subspecies differentiation. The virulence of F. tularensis differs between the subspecies. The F. tularensis subspecies (ssp.) tularensis is highly pathogenic, whereas the subspecies holarctica displays lower virulence and subspecies novicida and F. tularensis ssp. mediasiatica are hardly virulent. To differentiate the Francisellaceae and the F. tularensis-subspecies, an in-house Francisella library was built with the Bruker Biotyper system and validated together with the existing Bruker databases. In addition, specific biomarkers were defined based on the main spectra of the Francisella strains supplemented with in silico genome data. Our in-house Francisella library accurately differentiates the F. tularensis subspecies and the other Francisellaceae. The biomarkers correctly differentiate the various species within the genus Francisella and the F. tularensis subspecies. These MALDI-TOF MS strategies can successfully be applied in a clinical laboratory setting as a fast and specific method to identify F. tularensis to subspecies level.

Reliable quantification of citrate isomers and isobars with direct-infusion tandem mass spectrometry

Direct-infusion tandem mass spectrometry (DI-MS/MS) is an excellent tool for large cohort high-throughput quantitative metabolomics, MS imaging and single cell studies but incapable of discriminating isomers/isobars with similar MS spectral features. With experimental and density-functional theory (DFT) approaches, here, we comprehensively investigated the fragmentation pathways and characteristics of differential ion-mobility spectrometry (DMS) for three citrate isomers (citrate, isocitrate, glucaro-1,4-lactone) and an isobar (quinate) co-existing in biological sample such as urine. Results showed that all these compounds gave better MS spectra in negative-ion mode than positive-ion one and had numerous fragment ions under collision-induced dissociation (CID) with sequential losses of H2O and CO2. All observed fragment ions were assignable by combining experimental with DFT calculation results. A DI-DMS-MS/MS method was then developed to simultaneously quantify these four isomers/isobars with m/z 191–87 (CoV, −5.5 V), 191–73 (CoV, −3.5 V), 191–85 (CoV, −29.5 V) and m/z 191–93 (CoV, −41.5 V) for citrate, isocitrate, glucaro-1,4-lactone and quinate, respectively. The low limit-of-quantification was below 5.5 nM whilst accuracy was above 94% for all above compounds. The urinary concentrations of them in human and C57BL/6 mouse samples were further quantified showing clear inter-individual and inter-species level differences with significantly higher levels of isocitrate, glucaro-1,4-lactone and quinate in human urine samples than mouse ones. This provides an approach to understand the detailed fragmentation pathways for organic isomers/isobars and a high-throughput MS strategy to quantify them in complex mixtures for metabolomics, lipidomics, foodomics and exposomics especially when chromatographic separations are not useable.

Target-allele-specific probe single-base extension (TASP-SBE): a novel MALDI-TOF-MS strategy for multi-variants analysis and its application in simultaneous detection of α-/β-thalassemia mutations.

Single-nucleotide variants (SNVs) and copy number variations (CNVs) are the most common genomic variations that cause phenotypic diversity and genetic disorders. MALDI-TOF-MS is a rapid and cost-effective technique for multi-variant genotyping, but it is challenging to efficiently detect CNVs and clustered SNVs, especially to simultaneously detect CNVs and SNVs in one reaction. Herein, a novel strategy termed Target-Allele-Specific Probe Single-Base Extension (TASP-SBE) was devised to efficiently detect CNVs and clustered SNVs with MALDI-TOF-MS. By comprehensive use of traditional SBE and TASP-SBE strategies, a MALDI-TOF-MS assay was also developed to simultaneously detect 28 α-/β-thalassemia mutations in a single reaction system, including 4 α-thalassemia deletions, 3 HBA and 21 HBB SNVs. The results showed that all 28 mutations were sensitively identified, and the CNVs of HBA/HBB genes were also accurately analyzed based on the ratio of peak height (RPH) between the target allele and reference gene. The double-blind evaluation results of 989 thalassemia carrier samples showed a 100% concordance of this assay with other methods. In conclusion,a one-tube MALDI-TOF-MS assay was developed to simultaneously genotype 28 thalassemia mutations. This novel TASP-SBE was also verified a practicable strategy for the detection of CNVs and clustered SNVs, providing a feasible approach for multi-variants analysis with MALDI-TOF-MS technique.

Cutting-edge mass spectrometry strategy based on imaged capillary isoelectric focusing (icIEF) technology for characterizing charge heterogeneity of monoclonal antibody

Imaging capillary isoelectric focusing (icIEF) technology has been becoming the gold criteria of monitoring monoclonal antibody (mAb) charge heterogeneity that is one of the major product-related variants in recombinant biopharmaceuticals, since the first commercial instrument developed twenty years ago. However, the protein identification in icIEF separation is just based on isoelectric point (pI) measurement of protein. Although high resolution mass spectrometry (HRMS) is currently the most powerful means of qualitative protein analysis, traditional icIEF cannot compatibly be used in conjunction with MS due to the use of less volatile reagents. In addition, protein heterogeneity characterization in depth such as peptide mapping by high performance liquid chromatography (HPLC) requires the focused protein bands to be collected as fractions after the icIEF separation, which is a great challenge in biopharmaceutical discovery. In this work, pembrolizumab was employed as targeting mAb (a highly selective anti-PD-1 humanized mAb), an integrated icIEF platform was developed including analytical profiling, MS coupling and fraction collections for charged variant preparation. Multiple operation modes can be rapidly and flexibly switched just by changing customized capillary separation cartridges without more configurations. Main component, four acidic variants (A1-A4) and three basic variants (B1–B3) were baseline separated then directly detected by icIEF-HRMS online coupling for rapid screening of intact protein heterogeneity where reliable and accurate molecular weight of protein charged variants were obtained. Next, by installing preparative capillary separation cartridge, fractions of major charge variants (A2-3 and B1-2) and main component were collected for following LC-MS peptide mapping characterization. The whole workflow of icIEF-based MS strategy for protein heterogeneity is straight forward, reliable and accurate, which provides a comprehensive and revolutionary technology for protein drug quality control (QC) monitoring, MS coupling for fingerprinting intact protein and HPLC-MS peptide mapping in depth.

High-performance micro/nanoplastics characterization by MALDI-FTICR mass spectrometry

Micro/nanoplastics (MNPs) are widespread environmental pollutants that cause high health risks. However, high heterogeneity in particle sizes and chemical compositions of MNPs make their accurate characterization extremely challenging. Herein, we established a matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS) strategy for the unambiguous characterization of different types of MNPs with high performance, including polystyrene, polyethylene glycol terephthalate, polyamide, polymethyl methacrylate, acrylonitrile butadiene styrene copolymer, and polycarbonate. The MNP sample preparation and detection conditions were systematically optimized by using response surface methodology, and the MS detection signal-to-noise ratios were improved 1.5 times on average. The ultrahigh mass resolution of FTICR MS is crucial to the unambiguous elucidation of MNP structures. We demonstrate that this MS strategy is highly efficient in the characterization of polymer constitutions of environmental MNPs derived from foam, bottles, cable ties, and compact discs, providing a promising tool for MNP detection and safety evaluation.

Selective extraction of synthetic cathinones new psychoactive substances from wastewater, urine and cocktail using dummy molecularly imprinted polymers

Dummy molecularly imprinted polymers (DMIPs) for selective extraction of five common synthetic cathinones (SCs) were prepared by bulk polymerization. DMIPs materials possessed narrow diameter distribution (30–60 µm) and large specific surface area (329.6 m2 g-1). Imprinting factors for cathinone, methcathinone, mephedrone, methylone and ethylone were 1.11–1.82. DMIPs could also quickly adsorb SCs from aqueous solutions within 5 min. Therefore, the materials were used as solid-phase extraction (SPE) sorbents to selectively extract five SCs in complex samples. An accurate and sensitive analytical method based on DMIPs-SPE combined with HPLC-MS/MS was established. Under optimal conditions, the established method showed low limits of detection (0.002–0.1 ng mL-1), satisfactory recoveries (84.1–97.7%) and good repeatability (relative standard deviation (RSD) below 9%). The method was successfully verified using wastewater, urine and cocktail samples. Recoveries of SCs at three spiking levels were in the range of 75.1–98.6%, with RSD values below 7.0%. Compared with commercial sorbents, DMIPs showed better clean-up ability with matrix effect values of −24.1%–8.3% for all SCs in wastewater, urine and cocktail samples. Therefore, the developed DMIPs-SPE-HPLC-MS/MS strategy could be used as a specific and cost-effective method for sensitive determination of SCs in complex samples.

Systematic Identification of Bioactive Compositions in Leaves of Morus Cultivars Using UHPLC-ESI-QTOF-MS/MS and Comprehensive Screening of High-Quality Resources

Morus spp. leaves (MSLs) show various beneficial effects in the treatment of metabolic-related diseases, which have created a growing interest in MSL development as dietary supplements and functional foods. The illustration of chemical compositions and screening of high-quality MSL resources are therefore necessary for further application. This study developed a new UHPLC-ESI-QTOF-MS/MS strategy of in-source collision-induced dissociation (IS-CID) and target collision-cell CID (TCC-CID) to quickly capture analogues with consistent skeleton, and combined global natural product social molecular networking (GNPS) to efficiently annotate bioactive phytochemicals in MSLs. For the results, 49 bioactive ingredients, including quercetin-type flavonoids, kaempferol-type flavonoids, chlorogenic acid isomers, 1-deoxynojirimycin, γ-aminobutyric acid, amino acids, and unsaturated fatty acids, were systematically identified in MSLs for the first time. Quantification for the typical components was simultaneously carried out in MSLs of 90 Morus resources collected from different locations. Partial least squares discriminant analysis (PLS-DA) indicated that quercetin-3-O-(6″-O-malonyl)-glucoside, rutin, kaempferol-3-O-(6″-O-malonyl)-glucoside, kaempferol-3-O-rutinoside, and chlorogenic acid showed high variable importance in the project (VIP > 1) that were significant constituents for the differences between MSL species. Then, high-quality MSLs were comprehensively screened in multiple Morus cultivars based on the criteria importance through intercriteria correlation (CRITIC) method. This study presented an efficient strategy to annotate bioactive compounds, revealed the difference of bioactive components in MSLs, and provided important information for the high-value production of Morus cultivars in food and supplement fields.

Development of a GC–MS strategy for the determination of cross-linked proteins in 20th century paint tubes

In this paper we present the technical study of protein-drying oil mixtures in the paint formulation of original manufacturers paint tubes from Fabbrica di colori per Belle Arti Maimeri dating back to the 1950s. The study is part of a wider research project aimed at understanding the chemistry of protein-drying oil mixtures, and how the oil curing in the presence of proteins may affects the protein analysis with mass spectrometric based techniques.Tempera grassa, according to traditional Late Medieval and Renaissance painting techniques, entails the use, as paint binder, of a mixture of a drying oil with a water miscible medium, commonly egg. The paints analysed in this study were, according to technical documentation available at the manufacturer, based on a mixture of linseed oil, ovalbumin and mastic resin. All the components of the paints were detected but proteins proved very challenging. They could not be detected by pyrolysis coupled to gas chromatography-mass spectrometry, nor by using classical procedures for gas chromatography – mass spectrometry analysis of amino acids after hydrolysis. A new analytical procedure based on two subsequent hydrolysis steps assisted by microwaves was implemented and proved to be successful. The first step with trifluoroacetic acid was aimed at a partial hydrolysis of proteins into peptides, for their efficient extraction. The second with hydrochloric acid in the vapour phase was used for a complete hydrolysis of peptides into amino acids for the GC–MS analysis. Linking experimental results on the tempera grassa paints to data obtained on the curing of oil/protein mixtures in paint mock-ups, the hypothesis that copolymerisation of proteins and the oil has taken place is proposed, and a discussion on how this may affect protein detection is carried out.

Comprehensive analysis of O-glycosylation of amyloid precursor protein (APP) using targeted and multi-fragmentation MS strategy

BackgroundThe aberrant proteolytic processing of amyloid precursor protein (APP) into amyloid β peptide (Aβ) in brain is a critical step in the pathogenesis of Alzheimer's disease (AD). As an O-glycosylated protein, O-glycosylation of APP is considered to be related to Aβ generation. Therefore, comprehensive analysis of APP O-glycosylation is important for understanding its functions. MethodsWe developed a Targeted MS approach with Multi-Fragmentation techniques (TMMF strategy), and successfully characterized O-glycosylation profiling of APP695 expressed in HEK-293 T cells. We calculated relative abundance of glycopeptides with various O-glycosites and O-glycans, and further investigated the alteration of APP O-glycosylation upon TNF-α treatment. ResultsA total of 14 O-glycosites were identified on three glycopeptides of APP, and at least four O-glycans including GalNAc (Tn antigen), core 1, and mono−/di-sialylated core 1 glycans were determinant at the residues of Thr576 and Thr577. We found a dense cluster of truncated O-glycans on the region nearby beginning of E2 domain and high abundance of sialylated O-glycans on the region close to β-cleavage site. Moreover, we also observed that TNF-α could upregulate the expression of APP and the truncated O-glycans on APP in HEK-293 T cell. ConclusionOur study established an intact O-glycopeptide MS analysis strategy for APP O-glycopeptide identification with enhanced fragmentation efficiency and detection sensitivity. These results provide a comprehensive O-glycosylation map of APP expressed in HEK-293 T cell. General significanceThe accurate O-glycosites and O-glycan structures on APP may lead to a better understanding of the roles O-glycosylation plays in the processing and functions of APP.

Optimized MALDI-TOF MS Strategy for Characterizing Polymers.

In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) plays an essential role in the analysis of polymers. To acquire a more reliable strategy for polymer profiling, we characterized four representative polymers including polyethylene glycol 6000, polyvinylpyrrolidone K12, polymer polyol KPOP-5040, and polyether polyol DL-4000. The preparation methods of these four polymer samples have been optimized from six aspects, including matrix, cationization reagent, solvent, mixing ratio of cationization reagent to polymer, mixing ratio of matrix to polymer, and laser intensity. After investigating the effects of seven commonly used matrices on the ionization efficiency of four polymers, trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene] malononitrile (DCTB) was found to be the only matrix suitable for the analysis of all the four polymers. Our experimental results suggested that different polymers showed a certain preference for different cationization reagents. For example, the polymer polyol KPOP-5040 was suitable for sodium iodide as the cationization reagent, while polyvinylpyrrolidone K12 was more suitable for silver trifluoroacetate (AgTFA). For the choice of solvent, tetrahydrofuran is a reagent with rapid evaporation and a wide range of dissolution which can achieve the best results for the analysis of four polymers. The optimized method was successfully applied to the identification of DSPE-PEG-NH2 with different polymerized degrees. This MALDI-TOF strategy potentially provided the supplementary function through the polymer’s application in biomedical and visible probing.

Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues.

From a general public health perspective, a strategy combining non-targeted and targeted lipidomics MS-based approaches is proposed to identify disrupted patterns in serum lipidome upon growth promoter treatment in pigs. Evaluating the relative contributions of the platforms involved, the study aims at investigating the potential of innovative analytical approaches to highlight potential chemical food safety threats. Serum samples collected during an animal experiment involving control and treated pigs, whose food had been supplemented with ractopamine, were extracted and characterised using three MS strategies: Non-targeted RP LC-HRMS; the targeted Lipidyzer™ platform (differential ion mobility associated with shotgun lipidomics) and a homemade LC-HRMS triglyceride platform. The strategy enabled highlighting specific lipid profile patterns involving various lipid classes, mainly in relation to cholesterol esters, sphingomyelins, lactosylceramide, phosphatidylcholines and triglycerides. Thanks to the combination of non-targeted and targeted MS approaches, various compartments of the pig serum lipidome could be explored, including commonly characterised lipids (Lipidyzer™), triglyceride isomers (Triglyceride platform) and unique lipid features (non-targeted LC-HRMS). Thanks to their respective characteristics, the complementarity of the three tools could be demonstrated for public health purposes, with enhanced coverage, level of characterization and applicability.

STRATEGIES FOR HEPATOCYTE DIFFERENTIATION DERIVED FROM INDUCED PLURIPOTENT STEM CELLS USING SPHEROIDS

<h3>Background/Objective</h3> One of the main cells in the liver is the hepatocyte, which regulates the metabolism of various nutrients and xenobiotics, mediates endocrine function and excretion of toxic substances. Hepatocytes function in vitro have been studied for many years using primary hepatocytes and immortalized cells. Nevertheless, these cells show phenotypic instability or loss of adult liver functions and altered expression of important transcription factors. As an alternative to obtain a stable genetic background with preserved function and in large quantities, hepatocytes are being generated through differentiation of induced pluripotent stem cells (iPSC). However, one of the main problems to be overcome is the phenotype maturation. In this context, the objective of this work was to compare two different hepatocyte differentiation protocols using spheroids derived from iPSC. <h3>Methods</h3> Immunofluorescence for OCT3/4 and Nanog was performed to characterized pluripotent phenotype of iPSC and hepatocyte differentiation was induced for 28 days (D28). Two plating strategies were adopted to form the definitive endoderm: iPSC-monolayers (M) and iPSC-spheroids (S). To induce definitive endoderm, activin A and CHIR99021 were added to both plating conditions for 5 days. Prior hepatic maturation, iPSC-monolayers were also aggregated to form spheroids (MS). Subsequently, HGF and SB431542 were added to MS and S medium for 23 days. Spheroids were evaluated by real time PCR and immunofluorescence for hepatocyte-specific markers at D28. <h3>Results</h3> At protein level, the iPSC showed a pluripotent character through the nuclear presence of OCT3/4 and NANOG. At the end of the differentiation protocol, S differentiation strategy exhibited contractile cells. Albumin and cardiac troponin T were detected into the same spheroid by immunofluorescence. The MS strategy showed no beating cells. Also, CYP3A4 and albumin were detected by immunofluorescence and detectable mRNA levels were expressed for HNF4α, transferrin and alpha-1 antitrypsin. <h3>Conclusions</h3> Hepatocyte differentiation using spheroids requires a monolayer endoderm formation step in order to avoid the presence contractile cells at the end of protocol. Moreover, spheroid cells exhibited a great mature hepatocyte phenotype and can be used as a powerful tool for cell therapy, liver bioengineering, studies of drug efficacy and toxicity assays.

Detection, Mapping, and Proteotyping of SARS-CoV-2 Coronavirus with High Resolution Mass Spectrometry.

A high resolution mass spectrometry approach has been applied for the first time to detect and characterize SARS-CoV-2 coronavirus in cell cultured and nasopharyngeal swab specimens. Peptide ions for three of the most abundant structural viral proteins (membrane, nucleocapid, and spike) are detected and assigned directly, by virtue of the high resolution and mass accuracy within the mass maps of whole virus digests, without the need for tandem mass spectrometry (MS/MS). MALDI-MS based approaches offer high sample throughput and speed, compared with those of LC–MS strategies, and detection limits at some 105 copies, or orders of magnitude less with selected ion monitoring, that compete favorably with conventional reverse transcription polymerase chain reaction (RT-PCR) strategies. The detection of signature peptides unique to SARS-CoV-2 coronavirus over those from the influenza virus allows for its unambiguous detection.

C60-based chemical labeling strategy for the determination of polyamines in biological samples using matrix-assisted laser desorption/ionization mass spectrometry

Bioactive polyamines play important roles in many biological processes such as gene expression, cell growth, protein synthesis, and signal transduction. Accurate determination of polyamines is helpful for studying their biological functions. Herein, a C60-based chemical labeling strategy was proposed for the determination of polyamines (putrescine, cadaverine, spermidine, and spermine) in biological samples using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). An N-hydroxysuccinimide ester functionalized C60 (NHS–C60) was used as a labeling reagent and the m/z of the labeled polyamines reached up to more than 900 Da, which avoided matrix interferences in the low m/z region. In addition, as NHS–C60 derivatives, mono- and bis-substituted polyamines were produced simultaneously, which benefited the qualitative analysis of polyamines. The analytical method was validated using NHS–C60 labeled polyamines in cells and mice feces samples. Good linearities were obtained with correlation coefficients ranging from 0.9786 to 0.9982. The limits of quantification were in the range of 0.68–1.48 pmol. Good reproducibility and reliability of our proposed method were confirmed by intra- and inter-day precisions ranged from 2.8 to 16.6%, and the recoveries ranged between 81.8 and 119.9%. Finally, the proposed method was applied to determine polyamines in cells and mice feces. Three polyamines were detected in the cells, and the contents of cadaverine and spermidine in the feces of high-fat diet mice were found to be significantly lower than those in the normal diet mice. The results show that the proposed NHS–C60 labeling coupled with MALDI MS strategy is suitable for the determination of polyamines in biological samples.

Discover and identify unknown alkylation DNA adducts induced by sulfonates using prediction driven -MRM-profiling strategy

Alkylated DNA adducts are the most important and common form of DNA damage at the molecular level. In addition to known alkylated DNA adducts, many unknown DNA adducts remain to be discovered. A prediction-driven MRM profiling MS strategy has been established for the rapid discovery of unknown DNA adducts induced by sulfonates. The innovative aspects and core of this strategy are the construction of the prediction MRM list, which includes 36 possible precursor ion and characteristic product ion transitions of DNA adducts based on MS fragmentation patterns, and then unknown DNA adducts 7-propyl guanine and 7-butyl guanine were discovered based on the diagnostic MRM signals of the DNA samples, and subsequently confirmed using high-resolution MS data and synthetic standards for the first time. Furthermore, DNA adducts, including newly found adducts in a human cell model and rat tissues after nitrosamine and sulfonate exposure, were unambiguously investigated by a UHPLC-MS/MS method. As a result, different alkyl methanesulfonates, including methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS), PMS and BMS, all lead to the formation of 7MeG in addition to their own specific alkylation DNA adducts. The ester group of the sulfonate determines the specific types of DNA adducts produced, and the sulfonate might undergo transesterification with the methyl donors that commonly exist in eukaryotic organisms such as SAM, resulting in the formation of MMS, which induce the generation of methyl DNA adducts after EMS, PMS and BMS exposure. Furthermore, similar DNA adduct profiles were presented in both human cells and rat tissues. This approach could be useful in the future for probing unknown DNA adducts and simultaneously profiling both known and unknown DNA adducts in both in vitro to in vivo settings to evaluate potential genotoxicities and cancer risks to populations exposed to genotoxins.