Determination of α-methylenecyclopropylglycine in Shahi and China litchi cultivars at three different maturity stages: A quantitative study using liquid chromatography tandem mass spectrometry.

This study presents the contents of α-methylenecyclopropylglycine, a potentially toxic amino acid, in the peel, pulp and seed fractions of two well-known litchi varieties, namely Shahi and China, over a span of three harvest-seasons. For analysing α-methylenecyclopropylglycine, an LC-MS/MS-based method was validated. The method-accuracies fell within 75-110 % (RSD, <15 %) at 0.1 mg/kg (LOQ) and higher levels. A comparative evaluation of the results in peel, pulp and seed at 30 days before harvest (DBH), 15-DBH, and edible-ripe stage revealed that α-methylenecyclopropylglycine content increased as the litchi seeds grew towards maturity, regardless of the cultivar. In arils, at maturity, the concentration of α-methylenecyclopropylglycine ranged from not-detected to 11.7 µg/g dry weight. The Shahi cultivar showed slightly higher α-methylenecyclopropylglycine content in comparison to China litchi. This paper presents the first known analysis of combined seasonal data on different fruit components at various growth stages for the two chosen litchi cultivars grown in India.

Identifying an Abnormal Phosphorylated Adaptor by Viral Kinase Using Mass Spectrometry.

Mass spectrometers are widely used to identify protein phosphorylation sites. The process usually involves selective isolation of phosphoproteins and subsequent fragmentation to identify both the peptide sequence and phosphorylation site. Immunoprecipitation could capture and purify the protein of interest, greatly reducing sample complexity before submitting it for mass spectrometry analysis. This chapter describes a method to identify an abnormal phosphorylated site of the adaptor protein by a viral kinase through immunoprecipitation followed by LC-MS/MS.

Direct analysis in real time mass spectrometry (DART-MS/MS) for rapid urine opioid detection in a clinical setting.

BACKGROUND AND AIMS: Current laboratory methods for opioid detection involve an initial screening with immunoassays which offers efficient but non-specific results and a subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmation which offers accurate results but requires extensive sample preparation and turnaround time. Direct Analysis in Real Time (DART) tandem mass spectrometry is evaluated as an alternative approach for accurate opioid detection with efficient sample preparation and turnaround time. MATERIALS AND METHODS: DART-MS/MS was optimized by testing the method with varying temperatures, operation modes, extraction methods, hydrolysis times, and vortex times. The method was evaluated for 12 opioids by testing the analytical measurement range, percent carryover, precision studies, stability, and method-to-method comparison with LC-MS/MS. RESULTS: DART-MS/MS shows high sensitivity and specificity for the detection of 6-acetylmorphine, codeine, hydromorphone, oxymorphone, hydrocodone, naloxone, buprenorphine, norfentanyl, and fentanyl in urine samples. However, its performance was suboptimal for norbuprenorphine, morphine and oxycodone. CONCLUSION: In this proof-of-concept study, DART-MS/MS is evaluated for its rapid quantitative definitive testing of opioids drugs in urine. Further research is needed to expand its application to other areas of drug testing.

Neuroglycome alterations of hippocampus and prefrontal cortex of juvenile rats chronically exposed to glyphosate-based herbicide.

Introduction: Glyphosate-based herbicides (GBHs) have been shown to have significant neurotoxic effects, affecting both the structure and function of the brain, and potentially contributing to the development of neurodegenerative disorders. Despite the known importance of glycosylation in disease progression, the glycome profile of systems exposed to GBH has not been thoroughly investigated. Methods: In this study, we conducted a comprehensive glycomic profiling using LC-MS/MS, on the hippocampus and prefrontal cortex (PFC) of juvenile rats exposed to GBH orally, aiming to identify glyco-signature aberrations after herbicide exposure. Results: We observed changes in the glycome profile, particularly in fucosylated, high mannose, and sialofucosylated N-glycans, which may be triggered by GBH exposure. Moreover, we found major significant differences in the N-glycan profiles between the GBH-exposed group and the control group when analyzing each gender independently, in contrast to the analysis that included both genders. Notably, gender differences in the behavioral test of object recognition showed a decreased performance in female animals exposed to GBH compared to controls (p < 0.05), while normal behavior was recorded in GBH-exposed male rats (p > 0.05). Conclusion: These findings suggest that glycans may play a role in the neurotoxic effect caused by GBH. The result suggests that gender variation may influence the response to GBH exposure, with potential implications for disease progression and specifically the neurotoxic effects of GBHs. Understanding these gender-specific responses could enhance knowledge of the mechanisms underlying GBH-induced toxicity and its impact on brain health. Overall, our study represents the first detailed analysis of N-glycome profiles in the hippocampus and PFC of rats chronically exposed to GBH. The observed alterations in the expression of N-glycan structures suggest a potential neurotoxic effect associated with chronic GBH exposure, highlighting the importance of further research in this area.

Fabrication of a molecularly imprinted polymer-based electrochemical sensor for the selective assay of antipsychotic drug clozapine and performance comparison with LC-MS/MS.

Clozapine (CLO) is an atypical antipsychotic drug indicated for the treatment of schizophrenia. The treatment effectiveness of CLO is better than that of other atypical antipsychotics, and it has the advantage of being able to determine its effectiveness by measuring its concentration in the patient's blood. Thus, sensitive, selective, and accurate determination of CLO in blood is highly significant for treatment monitoring. This study describes the design and fabrication of a molecularly imprinted polymer (MIP)-based electrochemical sensor for CLO determination. This is the first MIP-based electrochemical application in the literature for CLO determination. Employing the thermal polymerization approach, the MIP was formed on the glassy carbon electrode (GCE) using CLO as the template, trans-3-(3-Pyridyl)acrylic acid (3,3-TA) as the functional monomer, and the support of zinc oxide nanoparticles (ZnO NPs). Elaborate characterizations in terms of surface morphology and electrochemistry were performed via scanning electron microscopy (SEM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) methods. An indirect approach was employed to determine CLO in standard solution, real human biological samples, and tablet formulation, using 5 × 10-3 M [Fe(CN)6]3-/4- solution as the redox probe. The limit of detection (LOD) values for the standard solution and serum sample were calculated as 2.9 × 10-11 M and 6.01 × 10-12 M, respectively. These values and recovery studies confirmed the sensor's sensitivity and feasibility. The measurements in the presence of similarly structured compounds (olanzapine and quetiapine fumarate) verified the sensor's superior selectivity. Moreover, the developed sensor's performance was compared and verified using an LC-MS/MS method using the student's t-test and F-test.

A pilot study on the differential urine proteomic profile of subjects with community-acquired acute kidney injury who recover versus those who do not recover completely at 4 months after hospital discharge.

Background: Community-acquired acute kidney injury (CA-AKI) is a sudden structural damage and loss of kidney function in otherwise healthy individuals outside of hospital settings having high morbidity and mortality rates worldwide. Long-term sequelae of AKI involve an associated risk of progression to chronic kidney disease (CKD). Serum creatinine (SCr), the currently used clinical parameter for diagnosing AKI, varies greatly with age, gender, diet, and muscle mass. In the present study, we investigated the difference in urinary proteomic profile of subjects that recovered (R) and incompletely recovered (IR) from CA-AKI, 4 months after hospital discharge. Methods: Study subjects were recruited from ongoing study of CA-AKI cohort. Patients with either sex or age > 18 years with no underline CKD were enrolled at the time of hospital discharge. Incomplete recovery from CA-AKI was defined as eGFR < 60 mL/min/1.73 m2 or dialysis dependence at 4 months after discharge. Second-morning urine samples were collected, and proteome analysis was performed with LC-MS/MS. Data were analyzed by Proteome Discoverer platform 2.2 (Thermo Scientific) using statistical and various bioinformatics tools for abundance of protein, cellular component, protein class and biological process were analyzed in the recovered and incompletely recovered groups. Results: A total of 28 subjects (14 in each group) were enrolled. Collectively, 2019 peptides and proteins with 30 high-abundance proteins in the incompletely recovered group (R/IR <0.5, abundance ratio adj. p-value <0.05) and 11 high-abundance proteins in the incompletely recovered group (R/IR >2.0, abundance ratio adj. p-value <0.05) were identified. Tissue specificity analysis, GO enrichment analysis, and pathway enrichment analysis revealed significant proteins in both the groups that are part of different pathways and might be playing crucial role in renal recovery during the 4-month span after hospital discharge. Conclusion: In conclusion, this study helped in identifying potential proteins and associated pathways that are either upregulated or downregulated at the time of hospital discharge in incompletely recovered CA-AKI patients that can be further investigated to check for their exact role in the disease progression or repair.

Detection, isolation and characterization of phage-host complexes using BONCAT and click chemistry.

Introduction: Phages are viruses that infect prokaryotes and can shape microbial communities by lysis, thus offering applications in various fields. However, challenges exist in sampling, isolation and accurate prediction of the host specificity of phages as well as in the identification of newly replicated virions in response to environmental challenges. Methods: A new workflow using biorthogonal non-canonical amino acid tagging (BONCAT) and click chemistry (CC) allowed the combined analysis of phages and their hosts, the identification of newly replicated virions, and the specific tagging of phages with biotin for affinity chromatography. Results: Replication of phage λ in Escherichia coli was selected as a model for workflow development. Specific labeling of phage λ proteins with the non-canonical amino acid 4-azido-L-homoalanine (AHA) during phage development in E. coli was confirmed by LC-MS/MS. Subsequent tagging of AHA with fluorescent dyes via CC allowed the visualization of phages adsorbed to the cell surface by fluorescence microscopy. Flow cytometry enabled the automated detection of these fluorescent phage-host complexes. Alternatively, AHA-labeled phages were tagged with biotin for purification by affinity chromatography. Despite biotinylation the tagged phages could be purified and were infectious after purification. Discussion: Applying this approach to environmental samples would enable host screening without cultivation. A flexible and powerful workflow for the detection and enrichment of phages and their hosts in pure cultures has been established. The developed method lays the groundwork for future workflows that could enable the isolation of phage-host complexes from diverse complex microbial communities using fluorescence-activated cell sorting or biotin purification. The ability to expand and customize the workflow through the growing range of compounds for CC offers the potential to develop a versatile toolbox in phage research. This work provides a starting point for these further studies by providing a comprehensive standard operating procedure.

Simultaneous determination of glyphosate, glufosinate and their metabolites in soybeans using solid-phase analytical derivatization and LC-MS/MS determination.

Glyphosate and glufosinate are the most widely used herbicides worldwide. We developed a simple and rapid analytical method for detecting glyphosate, glufosinate, and their metabolites (N-acetyl glyphosate: Gly-A, N-acetyl glufosinate: Glu-A, and 3-(hydroxymethylphosphinyl)propanoic acid: MPPA) in soybeans. The method involved extraction with water, trapping in a mini-column containing polymer-based resin with strong anion exchange groups, dehydration with acetonitrile, and solid-phase analytical derivatization at ambient temperature for 1 min using N-(tert-butyldimethylsilyl)-N-methyl trifluoroacetamide (MTBSTFA), followed by Liquid chromatography-tandem mass spectrometry (LC-MS/MS) determination. This method offers a straightforward and rapid analysis, using on-solid phase dehydration and rapid derivatization at an ambient temperature with MTBSTFA, yielding reliable results for glyphosate, glufosinate, and their metabolites. The method was applied to both domestic and imported soybean samples. Glyphosate, glufosinate, and Glu-A were detected in imported feed soybeans and processed soybean meal for feed use, reflecting the current conditions of GM soybean cultivation.

Development and validation of an LC-MS/MS method for simultaneous quantification of eight drugs in plasma and brain: Application in a pharmacokinetic study in mice.

A selective and sensitive liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method was developed and validated for simultaneous quantitation of a cassette of 8 drugs, including docetaxel, erlotinib, loperamide, riluzole, vemurafenib, verapamil, elacridar and tariquidar. Stable isotopically labeled compounds were available for use as internal standards for all compounds, except for tariquidar for which we used elacridar-d4. Sample pre-treatment involved liquid-liquid extraction using tert-butyl-methyl ether as this resulted in good recovery and low ion suppression. Chromatographic separation was achieved using a Zorbax Extend C18 analytical column and a linear gradient from 20 % to 95 % methanol in 0.1 % (v/v) formic acid in water. MS/MS detection using multiple reaction monitoring was done in positive ionization mode. We validated this assay for human and mouse plasma and mouse brain homogenates. The calibration curves were linear over a range 1-200 nM for each drug in the mix, except for tariquidar probably due to the lack of a stable isotope labeled analog. The intra-day and inter-day accuracies were within the 85-115 % range for all compounds at low, medium and high concentrations in the three different matrices. Similarly, the precision for all compounds at three different concentration levels ranged below 15 %, with the exception of tariquidar in mouse plasma and brain homogenate and riluzole in brain homogenate. Pilot studies have confirmed that the method is suitable for the analysis of mouse plasma samples and brain homogenates following cassette dosing of this mixture in mice.

Rapid Characterization of Phospholipids from Biological Matrix Enabled by Indium Tin Oxide (ITO) Coated Slide Assisted Enrichment MALDI Mass Spectrometry.

Lipidomic analysis of human serum is essential to monitor the individual's health status. Herein, we develop a facile strategy for rapid characterization of phospholipids in human serum via indium tin oxide (ITO) coated glass slide solid phase extraction MALDI mass spectrometry (ITO-SPE-MALDI-MS). Phospholipid species are retained on ITO slide via solid phase extraction owing to the unique property of the ITO material; the measurement of phospholipid species from 1 µl human serum within 2 min is achievable. A comparison of ITO-SPE strategy with conventional extraction methods was further carried out using liquid chromatography-mass spectrometry (LC-MS) and ion-mobility mass spectrometry (IM-MS), resulting in a comparable enrichment performance for the phospholipid analysis. Furthermore, rapid lipidomic profiling of serum samples from human colorectal cancer patients and cell lines was demonstrated. Our results indicate that ITO-SPE-MALDI-MS provides a higher throughput strategy for the analysis of phospholipid species in complex biological mixtures, showcasing its potential for applications in the analysis of clinical biofluids.

LC-MS/MS-QTOF dataset of chemical compounds detected in honey samples from Bali and Lombok, Indonesia.

Honey production is susceptible to manipulation by unscrupulous sellers, making honey authentication crucial to prevent fraud. The process of authenticating honey often necessitates the use of various analytical techniques, such as identifying the chemicals present in honey by means of hyphenated mass spectrometry. Here, we report on the investigation of the chemical composition of three honey samples collected at two locations in Lombok and Bali by liquid chromatography mass spectrometry (LC-MS). The three datasets include information regarding compound name, mass, retention times, as well as findings from database searches. Collectively, these data afford first insights into the compositional profile of honey samples from this specific geographical area.

Comparison of vancomycin assays in patients undergoing hemodialysis.

Vancomycin is a glycopeptide antibiotic mainly excreted by glomerular filtration. Therefore, patients undergoing hemodialysis tend to accumulate its crystalline degradation product, which has been associated with cross-reaction in commercial immunoassays. The aim of this study was to assess the performance of two commercial immunoassays for measuring vancomycin levels in patients undergoing hemodialysis. This method-comparison study enrolled patients undergoing hemodialysis at two hospitals in Porto Alegre, Brazil. Vancomycin serum concentrations measured by Chemiluminescent Microparticle Assay (CMIA) and measured by Kinetic Interaction of Microparticles in Solution (KIMS) were compared with Liquid Chromatography coupled with Tandem Mass Spectrometry (LC-MS/MS). A total of 64 samples from 42 patients and 54 samples from 23 patients were included in CMIA and KIMS groups. Both measurements were highly correlated with LC-MS/MS, with Spearman rank correlation coefficient r = 0.840 (p < 0.001) and r = 0.926 (p < 0.001), respectively. No deviation of linearity was observed (p = 0.81 and p = 0.49, respectively). The mean difference between CMIA and LC-MS/MS was -1.19 µg/mL and between KIMS and LC-MS/MS was -2.28 µg/mL. LC-MS/MS measured levels were, on average, 2.64 % higher than CMIA and 8.81 % higher than KIMS. CMIA and KIMS revealed accurate commercial methods to measure vancomycin serum concentrations in patients undergoing hemodialysis.

A broad-spectrum LC-MS/MS method for screening and quantification of 100 analytes in clinical and autopsy blood samples.

Liquid chromatography coupled with mass spectrometry (LC-MS) has been tremendously used for screening purposes in forensic toxicology, because of their great adaptability and reasonable time/resource consumption. Herein, a fully validated method based on liquid-liquid extraction (LLE) in human whole blood, by a multiple reaction monitoring (MRM) analysis through LC-MS/MS, is described. The proposed method simultaneously detects 100 analytes (plus three deuterated internal standard compounds) belonging to many different classes, including drugs of abuse, prescription and over-the-counter drugs commonly involved in poisoning and medical malpractice cases in our territory, as well as certain new psychoactive substances (NPS) and toxic substances potentially associated with adverse effects. The optimised LLE employs one extraction step of 200 µL blood using 0.1 M HCl methyl-tert-butyl-ether (MTBE) (acidified with concentrated HCl) proved to be suitable for the extraction of basic and neutral substances; as a reconstitution solvent a mixture of 88:12v/v, 0.1 % formic acid in 10 mM aqueous ammonium acetate, pH 3.5: 0.1 % formic acid in acetonitrile was used, yielding satisfactory recoveries for all analytes. The method was sensitive, showing low LOD/ LOQ for all substances ranging from 0.01 to 5/ 0.05-20 ng/mL, respectively. Linearity ranged between 0.05-500 ng/mL (R2 = 0.9811-0.9995), and the inter- and intra-day precisions ranged between 3-15 % and 7-18 %, respectively. Accuracy was evaluated in terms of percentage recovery, lying within acceptable range. The matrix effect expressed as ion suppression/enhancement of each analyte was in the range ±25 % for all analytes. Post-preparative stability of analytes was higher than 85 %, while no carryover between runs was observed. The developed method has been successfully applied in routine toxicological analyses for the analysis of biological samples from clinical and autopsy cases.

Non targeted and targeted LC-MS/MS insights into the composition and concentration of atmospheric microplastics and additives: Impacts and regional changes of sandstorms in Shanghai and Hohhot, China.

Increasing dust storms impact ecosystems and human health by resuspending dust and microplastics. Plastic pollution is a major global concern. This study examines the molecular composition and concentration of atmospheric microplastics and additives in Hohhot and Shanghai, China during dust and non-dust days using non-target and target LC-MS/MS analysis with Multiple Reaction Monitoring (MRM) methodology and a self-established plastic monomers database. In Hohhot, 98 microplastics and additives types were identified on dust days (41 unique) and 70 on non-dust days (10 unique), mainly PEG, HTPE, PET, PPG, and Nylon. The types fluctuate ranging from 35 to 65 due to dusty conditions. In Shanghai, 50 types were identified (no unique), with 25 to 30 types consistently present. Hohhot's microplastics concentration during dust days peaked at 3531.59 ng/m3, about three times higher than non-dust days (1669.17 ng/m3) and significantly higher than Shanghai's maximum of 589.85 ng/m3. Overall, microplastic monomers in both cities were mostly compounds with low unsaturation, indicating potential for long-term atmospheric persistence. Highly reactive monomers like HTPE, PEG, thrive on dust days in Hohhot due to insufficient light and strong winds. These conditions reduce photochemical reactivity, accelerate microplastic aging through collisions, and resuspend more microplastics from the soil, resulting in a wider variety of microplastics with different m/z and carbon contents during sandstorms. On non-dust days, microplastics have more concentrated m/z values, indicating that substances with similar chemical properties disperse more under normal conditions. These findings highlight the significant impact of dust storms on microplastics characteristics. SYNOPSIS: This study indicates that dust storms and regional differences can have significant impacts on the diversity and abundance of atmospheric microplastics.

Effects of Different Manufacturing Processes on Thermal and Photo-oxidative Stability of Sesame Oil.

The roasting process of sesame oil is expected to alter its internal composition and stability under oxidation condition. Presumably, the effect of roasting may differ with oxidation conditions (i.e., thermal and photo-oxidation), but such studies have not been undertaken. To further evaluate this notion, several type of sesame oils (raw and refined as unroasted oil, and roasted oil) and rapeseed oils as comparison were subjected to thermal oxidation (120℃) and photo-oxidation (50,000 lx) for 5 and 10 hours. The result revealed that the roasting sesame oil exhibited good stability under thermal oxidation, possibly due to the change on antioxidant agents such as sesamol and Maillard products during the roasting process. In contrast, the refined sesame oil (unroasted) demonstrated high stability under photo-oxidation, indicating that the refining process has a more significant impact on the oxidative stability in sesame oil compared to the alterations in its components caused by the roasting process. Taken together, this study is the first to show that the roasting and refining processes of sesame oil alter its internal composition and show different variations in sesame oils' oxidative stability under thermal and photo-oxidation, which holds significance considering its global consumption.

Long-term stability of five atypical antipsychotics (risperidone, olanzapine, paliperidone, clozapine, quetiapine) and the antidepressant mirtazapine in human serum assessed by a validated SPE LC-MS/MS method.

Long-term sample stability of five atypical antipsychoticdrugs risperidone, paliperidone, clozapine, quetiapine and olanzapine and the antidepressant drug mirtazapine in serum was studied by use of a newly developed and validated analytical method based on solid-phase extraction and liquid chromatography-tandem mass spectrometry. Ascorbic acid was used as an antioxidative agent to stabilize olanzapine during storage and sample preparation. We assessed analyte stability on long-term storage in serum samples at 25°C, 5°C, -20°C and -80°C, and during five freeze-thaw cycles. Analytes were stable for 23 days at room temperature except for olanzapine and mirtazapine (17 days). All analytes were stable for at least 30 days at 5°C. All analytes were stable for 270 days at -20°C, except for paliperidone and mirtazapine with 60 days and 180 days, respectively. All analytes were stable for 270 days at -80°C. Furthermore, all analytes were stable for five freeze-thaw cycles. We recommend storage at -80°C when samples drawn for analysis of antipsychotic drugs are stored for more than 60 days, whereas a temperature of -20°C is sufficient for storage less than 60 days.

Systematic synthesis and identification of monolignol pathway metabolites.

Monolignol serves as the building blocks to constitute lignin, the second abundant polymer on Earth. Despite two decades of diligent efforts, complete identification of all metabolites in the currently proposed monolignol biosynthesis pathway has proven elusive. This limitation also hampers their potential application. One of the primary obstacles is the challenge of assembling a collection of all molecules, because many are commercially unavailable or prohibitively costly. In this study, we established systematic pipelines to synthesize all 24 molecules through the conversions between functional groups on a core structure followed by the application to other core structures. We successfully identified all of them in Populus trichocarpa and Eucalyptus grandis, two representative species respectively from malpighiales and myrtales in angiosperms. Knowledge about monolignol metabolite chemosynthesis and identification will form the foundation for future studies.

Comprehensive phenolic profiling and biological evaluation of Centaurea glastifolia L. (Asteraceae).

The present investigation focused on the comprehensive analysis of the phenolic profile of Centaurea glastifolia L. (Asteraceae) and the assessment of its diverse biological activities. Utilising LC-MS/MS, the phytochemical composition of the 70% methanol extract of Centaurea glastifolia (CG-ME) was thoroughly elucidated, revealing the presence of 30 distinct phytochemical compounds. Notably, major phenolic constituents identified in the extract included quinic acid, chlorogenic acid, luteolin-7-O-glucoside, kaempferol-3-O-glucoside, luteolin, and apigenin-7-O-glucoside. The antioxidant, antibacterial, antiproliferative, and cytotoxic activities of CG-ME were investigated. The CG-ME exhibited a moderate capacity for scavenging DPPH radicals (IC50: 50.05 ± 1.58 µg/mL) and FRAP (63.96 ± 0.39 mg TE/g extract), indicating a moderate level of antioxidant activity. Moreover, CG-ME demonstrated significant antiproliferative effects (GI50: 1.10 and 1.30 µg/mL) on cancer cells (C6 and HTC cancer cell lines, respectively) while displaying low cytotoxicity towards normal cells (LC50: >1000 µg/mL). In terms of antibacterial activity, CG-ME was found to be inactive against tested both Gram-positive and Gram-negative bacterial strains (MIC > 500 µg/mL). The extracts had a promising antiproliferative effect on C6, HeLa, and HT29 cancer cell lines with a less cytotoxic effect (10.5-14.2%) against normal cells.

Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation.

Immunopeptidomics is the area of knowledge focused on the study of peptides assembled in the major histocompatibility complex (MHC), or human leukocyte antigen (HLA) in humans, which could activate the immune response via specific and selective T cell recognition. Advances in high-sensitivity mass spectrometry have enabled the detailed identification and quantification of the immunopeptidome, significantly impacting fields like oncology, infections, and autoimmune diseases. Current immunopeptidomics approaches primarily focus on workflows to identify immunopeptides from HLA molecules, requiring the isolation of the HLA from relevant cells or tissues. Common critical steps in these workflows, such as cell lysis, HLA immunoenrichment, and peptide isolation, significantly influence outcomes. A systematic evaluation of these steps led to the creation of an 'Immunopeptidome Score' to enhance the reproducibility and robustness of these workflows. This score, derived from LC-MS/MS datasets (ProteomeXchange identifier PXD038165), in combination with available information from public databases, aids in optimizing the immunopeptidome characterization process. The 'Immunopeptidome Score' has been applied in a systematic analysis of protein extraction, HLA immunoprecipitation, and peptide recovery yields across several tumor cell lines enabling the selection of peptides with optimal features and, therefore, the identification of potential biomarker and therapeutic targets.

Optimization of the determination of volatile organic compounds in plant tissue and soil samples: Untargeted metabolomics of main active compounds.

This review critically assesses the determination of low molecular weight volatiles by different methods, providing context for the development of suitable techniques to determine volatile content in plant tissue and soil samples as well as the associated analytical challenges. Although sensitive analytical methods have been reported in recent decades, studies on their application in modern investigative techniques are lacking. Herein, the latest sampling methods in volatile biochemistry, current advancements in the understanding of these analytes, and the significance of these findings for other types of volatiles are summarized. Gas chromatography, high-performance liquid chromatography, ion chromatography, thin-film microextraction, and real-time monitoring techniques are discussed and critically determined. This review concerns the methods most suitable for future research in this area.