Accurate Mass Research Articles

Four-Dimensional Lipidomic Analysis Using Comprehensive Online UHPLC × UHPSFC/Tandem Mass Spectrometry.

Multidimensional chromatography offers enhanced chromatographic resolution and peak capacity, which are crucial for analyzing complex samples. This study presents a novel comprehensive online multidimensional chromatography method for the lipidomic analysis of biological samples, combining lipid class and lipid species separation approaches. The method combines optimized reversed-phase ultrahigh-performance liquid chromatography (RP-UHPLC) in the first dimension, utilizing a 150 mm long C18 column, with ultrahigh-performance supercritical fluid chromatography (UHPSFC) in the second dimension, using a 10 mm long silica column, both with sub-2 μm particles. A key advantage of employing UHPSFC in the second dimension is its ability to perform ultrafast analysis using gradient elution with a sampling time of 0.55 min. This approach offers a significant increase in the peak capacity. Compared to our routinely used 1D methods, the peak capacity of the 4D system is 10 times higher than RP-UHPLC and 18 times higher than UHPSFC. The entire chromatographic system is coupled with a high-resolution quadrupole-time-of-flight (QTOF) mass analyzer using electrospray ionization (ESI) in both full-scan and tandem mass spectrometry (MS/MS) and with positive- and negative-ion polarities, enabling the detailed characterization of the lipidome. The confident identification of lipid species is achieved through characteristic ions in both polarity modes, information from MS elevated energy (MSE) and fast data-dependent analysis scans, and mass accuracy below 5 ppm. This analytical method has been used to characterize the lipidomic profile of the total lipid extract from human plasma, which has led to the identification of 298 lipid species from 16 lipid subclasses.

Paralytic Shellfish Poisoning (PSP) Toxins in Bivalve Molluscs from Southern Italy Analysed by Liquid Chromatography Coupled with High-Resolution Mass Spectrometry (UHPLC-HRMS/MS).

A new method for simultaneous determination by liquid chromatography coupled with high resolution mass spectrometry (UHPLC-HRMS/MS) of 14 paralytic shellfish poisoning toxins (PSP), that is, Saxitoxin, Neosaxitoxin, Gonyautoxins and their respective variants, in bivalve molluscs, is herein described. The samples were extracted by acetic acid solution, then analysed by UHPLC coupled with a Q-Exactive Orbitrap Plus high resolution mass spectrometer, by electrospray ionization mode (ESI) with no further clean up step. The analysis was carried out by monitoring both the exact mass of the molecular precursor ion of each compound (in mass scan mode, resolution at 70,000 FWHM) and its respective fragmentation patterns (two product ions) with mass accuracy greater than 5 ppm. The analytical performance of the method was evaluated calculating trueness, as mean recoveries of each biotoxin, between 77.8% and 111.9%, a within-laboratory reproducibility (RSDR) between 3.6% and 12.2%, the specificity, the linearity of detector response, and the ruggedness for slight changes The results of the validation study demonstrate this method fits for the purposes of the official control of PSP toxins in molluscs. The results of two years of monitoring in local mussel farms are also reported, showing that no significant concerns for food safety in the monitored productions.

Cosmography from accurate mass modeling of the lens group SDSS J0100+1818: Five sources at three different redshifts

Systems where multiple sources at different redshifts are strongly lensed by the same deflector allow one to directly investigate the evolution of the angular diameter distances as a function of redshift, and thus to learn about the geometry of the Universe. We present measurements of the values of the total matter density, $ m $, and of the dark energy equation of state parameter, $w$, through a detailed strong lensing analysis of SDSS J0100+1818, a group-scale system at $z=0.581$ with five lensed sources, from $z=1.698$ to $4.95$. We take advantage of new spectroscopic data from the Multi Unit Spectroscopic Explorer (MUSE) on the Very Large Telescope to securely measure the redshift of 65 sources, including the 5 multiply imaged background sources (lensed into a total of 18 multiple images) and 19 galaxies on the deflector plane, all employed to build robust strong lensing models with the software GLEE . The total mass distribution of the deflector is described in a relatively simple way, and includes an extended halo, the brightest group galaxy (BGG) with a measured stellar velocity dispersion of ($380.5 km.s^ $, and fainter members. We measure $ m $ in a flat Lambda cold dark matter (CDM) model, and $ m $ and $w = -1.27_ $ in a flat $w$CDM model. Given the presence of different sources angularly close in projection, we quantify through a multiplane approach their impact on the inferred values of the cosmological parameters. We obtain consistent median values, with uncertainties for only $ m $ increasing by approximately a factor of 1.5. Thanks to the remarkably wide radial interval where the multiple images are observed, ranging from 15 to 77 kpc from the BGG, we accurately measure the total mass profile and infer the stellar over total mass profile of the deflector. They result in a total mass of $(1.55 $ M$_ within 50 kpc and a stellar over total mass profile decreasing from <!PCT!>$ at the BGG effective radius to $(6.6 1.1) <!PCT!>$ at $R 77$ kpc. Our results confirm that SDSS J0100+1818 is one of the most massive (lens) galaxies known at intermediate redshift and one of the most distant candidate fossil systems. We also show that group-scale systems that act as lenses for $ 3$ background sources at different redshifts enable one to estimate the values of the cosmological parameters $ m $ and $w$ with an accuracy that is competitive with that obtained from lens galaxy clusters.

Chemical Composition of Aerosols from the E-Cigarette Vaping of Natural and Synthetic Cannabinoids.

Vaping cannabinoids in electronic (e)-cigarette devices is rapidly increasing in popularity, particularly among adolescents, although the chemistry affecting the composition of the vape aerosol is not well understood. This work investigates the formation of aerosol mass, bioactive hydroxyquinones, and harmful or potentially harmful carbonyls from the e-cigarette vaping of natural and synthetic cannabinoids e-liquids in propylene glycol and vegetable glycerin (PG/VG) solvent at a 50 mg/mL concentration in a commercial fourth-generation vaping device. The following cannabinoids were studied: cannabidiol (CBD), 8,9-dihydrocannabidiol (H2CBD), 1,2,8,9-tetrahydrocannabidiol (H4CBD), cannabigerol (CBG), and cannabidiolic acid (CBDA). Quantification of analytes was performed using liquid chromatography coupled to accurate mass spectrometry. The addition of cannabinoids significantly increased aerosol and carbonyl formation compared with the PG/VG solvent alone. All cannabinoids in the study formed hydroxyquinones during vaping (up to ∼1% mass conversion) except for CBDA, which primarily decarboxylated to CBD. Hydroxyquinone formation increased and carbonyl formation decreased, with a decreasing number of double bonds among CBD and its synthetic analogues (H2CBD and H4CBD). During the vaping process, ∼3-6% of the cannabinoid mass can be observed as carbonyls under the study conditions. Oxidation of the terpene moiety on the cannabinoids is proposed as a major contributor to carbonyl formation. CBD produced significantly higher concentrations of formaldehyde, acetaldehyde, acrolein, diacetyl, and methylglyoxal compared with the other cannabinoid samples. CBG produced significantly higher levels of acetone, methacrolein, and methylglyoxal. Conversion of CBD to tetrahydrocannabinol (THC) was not observed under the study conditions. The chemical mechanism basis for these observations is discussed. Compared with other modalities of use for CBD and other cannabinoids, vaping has the potential to adversely impact human health by producing harmful products during the heated aerosolization process.

UHPLC-QTOFMS Urine Drug Screening With Dilute-and-Shoot Sample Preparation and Vacuum-Insulated Probe-Heated Electrospray Ionization.

We developed a method for comprehensive urine drug screening by applying dilute-and-shoot extraction and vacuum-insulated probe-heated electrospray ionization with ultra-high performance liquid chromatography high-resolution quadrupole time-of-flight mass spectrometry (DS-UHPLC-VIP-HESI-QTOFMS). The method involved five-fold post-hydrolysis dilution of urine samples and chromatography on a C18 UHPLC column prior to QTOFMS analysis. The recently introduced VIP-HESI ion source was chosen due to its enhanced ionization efficiency and compatibility with UHPLC-QTOFMS. Extensive data was acquired in positive ion mode with a low collision energy (7 eV) and an elevated collision energy (30 eV), using the broadband collision-induced dissociation data acquisition scan mode that continuously generated high-resolution and accurate mass for parent and fragment qualifier ions, and parent ion isotopic patterns. Compound identification was performed against an in-house database with 1263 compound entries, using an automated post-run reverse target database search with preset identification criteria. Method validation with 56 different drugs showed acceptable results for the limit of identification (median 5 ng/mL), matrix effects (70-130%), repeatability of retention times (< 1%), mass accuracy (< 1 mDa), as well as for specificity and stability. As compared with an established UHPLC-QTOFMS method relying on solid-phase extraction and conventional electrospray ionization, DS-UHPLC-VIP-HESI-QTOFMS produced comparable results from authentic clinical urine samples for most drugs, but showed clearly improved detectability for pregabalin, gabapentin, and ritalinic acid. We anticipate that the new method will be a step forward for laboratories performing routine urine drug screening due to its fast turnaround time, reduced manual workload, cost efficiency, and broad substance coverage.

A Proteomics Pipeline for Generating Clinical Grade Biomarker Candidates from Data-Independent Acquisition Mass Spectrometry (DIA-MS) Discovery.

Clinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package that uses data-independent acquisition analysis from a discovery cohort to select precursors, peptides, and proteins that adhere to analytical criteria required for established targeted assays. TEAQ was applied to DIA-MS data from plasma samples acquired on a new high resolution accurate mass (HRAM) mass spectrometry platform where precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra-protein correlation based on 8- or 11-point loading curves at three throughputs. This data can be used as a general resource for developing other targeted assays. TEAQ analysis of data from a case and control cohort for inflammatory bowel disease (n=492) identified 1110 signature peptides for 326 quantifiable proteins from the 1179 identified proteins. Applying TEAQ analysis to discovery data will streamline targeted assay development and the transition to validation and clinical studies.

A Proteomics Pipeline for Generating Clinical Grade Biomarker Candidates from Data‐Independent Acquisition Mass Spectrometry (DIA‐MS) Discovery

AbstractClinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package that uses data‐independent acquisition analysis from a discovery cohort to select precursors, peptides, and proteins that adhere to analytical criteria required for established targeted assays. TEAQ was applied to DIA‐MS data from plasma samples acquired on a new high resolution accurate mass (HRAM) mass spectrometry platform where precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra‐protein correlation based on 8‐ or 11‐point loading curves at three throughputs. This data can be used as a general resource for developing other targeted assays. TEAQ analysis of data from a case and control cohort for inflammatory bowel disease (n=492) identified 1110 signature peptides for 326 quantifiable proteins from the 1179 identified proteins. Applying TEAQ analysis to discovery data will streamline targeted assay development and the transition to validation and clinical studies.

Targeted and Untargeted Amine Metabolite Quantitation in Single Cells with Isobaric Multiplexing.

We developed a single cell amine analysis approach utilizing isobarically multiplexed samples of 6 individual cells along with analyte abundant carrier. This methodology was applied for absolute quantitation of amino acids and untargeted relative quantitation of amines in a total of 108 individual cells using nanoflow LC with high-resolution mass spectrometry. Together with individually determined cell sizes, this provides accessible quantification of intracellular amino acid concentrations within individual cells. The targeted method was partially validated for 10 amino acids with limits of detection in low attomoles, linear calibration range covering analyte amounts typically from 30 amol to 120 fmol, and correlation coefficients (R) above 0.99. This was applied with cell sizes recorded during dispensing to determine millimolar intracellular amino acid concentrations. The untargeted approach yielded 249 features that were detected in at least 25 % of the single cells, providing modest cell type separation on principal component analysis. Using Greedy forward selection with regularized least squares, a sub-selection of 100 features explaining most of the difference was determined. These features were annotated using MS2 from analyte standards and accurate mass with library search. The approach provides accessible, sensitive, and high-throughput method with the potential to be expanded also to other forms of ultrasensitive analysis.

Kinetic study, byproducts characterization and photodegradation pathway of profoxydim in a biochar water soil system

The study focused on the photodegradation of profoxydim, a low-toxicity cyclohexanedione herbicide commonly used in rice crops, under simulated sunlight conditions. Profoxydim’s behavior in paddy field conditions is not well understood, and this research aimed to fill that gap, particularly examining the effect of commonly utilized organic amendments such as biochar (BC) on its degradation. Results indicated that profoxydim degrades rapidly, with a half-life of 2.4 ± 0.3 h in paddy water and 1.03 ± 0.1 h in paddy soil. However, when BC was introduced, the degradation slowed significantly, extending the half-lives to 3.1 ± 0.2 h in water and 3.07 ± 0.5 h in soil. The study identified five degradation products (DPs) using TOF mass accuracy measurements and MS/MS spectra fragmentation. Two of these DPs were found to be more stable than profoxydim itself. Additionally, the research proposed a novel photodegradation pathway, highlighting processes such as homolytic C-N bond cleavage, photoisomerization, and photoinduced oxidation. The study’s findings contribute new insights into the environmental fate of profoxydim, offering a deeper understanding of its transformation in rice paddy fields and aiding in the assessment of potential risks associated with its residues in agricultural environments.

Systematic Characterisation of the Fragmentation of Flavonoids Using High-Resolution Accurate Mass Electrospray Tandem Mass Spectrometry.

Flavonoids are a class of polyphenolic secondary metabolites found in plants. Due to their ubiquity in our daily dietary intake and their major anti-oxidative, anti-inflammatory and anti-mutagenic activities, they have been a major focus of wide-ranging research for the past two decades. Mass spectrometry combined with liquid chromatography is one of the most popular techniques for the analysis of flavonoids. In this study, high-resolution accurate mass electrospray tandem mass spectrometry was used to study 30 flavonoids in both positive and negative ionisation modes. From the data obtained, common losses were summarised and compiled. Dominating neutral losses were tabulated. The radical loss of CH3· was observed in flavonoids containing methoxy groups and three key diagnostic product ions were identified. These were m/z 153 (indicative of two OH groups on ring A) m/z 167 (indicative of one OH and one methoxy group on ring A) and m/z 151 (a flavanol, with no ketone oxygen but two OH groups on ring A). These will be useful in structural elucidation of unknown flavonoids and flavonoid metabolites. Energy breakdown graphs were utilised to distinguish between three pairs of structural isomers, and to help rationalise proposed fragmentation pathways. Lastly, a competition of loss of CH3· and methane was reported for rhamnetin and isorhamnetin in the negative ion mode for the first time. Proposed fragmentation pathways were given to rationalise the differences in peak intensities for this competitive process.

Development and validation of an LC‒MS/MS method for the determination of cyclocreatine phosphate and its related endogenous biomolecules in rat heart tissues

The cardioprotective drug cyclocreatine phosphate has been awarded Food and Drug Administration-orphan drug designation for the prevention of ischemic injury to enhance cardiac graft recovery and survival in heart transplantation. Cyclocreatine phosphate is the water-soluble derivative of cyclocreatine. Estimating the levels of Cyclocreatine phosphate, Adenosine triphosphate, Creatine Phosphate, Creatine and Cyclocreatine helps us in understanding the energy state as well as evaluating the heart cells’ function. The quantification of endogenous compounds imposes a challenging task for analysts because of the absence of a true blank matrix, whose use is required according to international guidelines. Recently, the International Council for Harmonization issued a new guideline that contains guidance on the validation of methods used to quantify endogenous components, such as the background subtraction approach that was employed in our current study. Specifically, we developed and validated a sensitive, reliable and accurate liquid chromatography-tandem mass spectrometry assay to determine simultaneously the levels of mentioned endogenous compounds in rat heart tissue. Tissue samples were prepared by protein precipitation extraction using water: methanol (1:1). Using Ultra Performance Liquid Chromatography, Chromatographic separation was achieved with ZORBAX Eclipse Plus C18 4.6 × 100 mm,3.5 μm column and conditions as following: ammonium acetate (pH 8.5): acetonitrile, 70:30 mobile phase, 0.7 mL/min flow rate and 25 °C temperature. Electrospray ionization mass detector with Multiple reaction monitoring mode was then employed, using both positive and negative modes, Analysis was carried out using 5.00–2000.00 ng/mL linear concentration range within 2 min for each analyte. According to Food and Drug Administration guidelines for bioanalytical methods, validation was carried out. We investigated the matrix effect, recovery efficiency and process efficiency for the analyte in neat solvent, postextraction matrix and tissue. The results stated mean percentage recoveries higher than 99%, accuracy 93.32–111.99%, and Relative Standard Deviation (RSD) below 15% within the concentration range of our study which indicated that target analytes’ stability in their real matrix is sufficient under the employed experimental conditions.

A one-field fluid/meso-structure coupling approach for multiscale transport in heterogeneous porous media

Modeling transport phenomena within heterogeneous porous media poses considerable challenges, particularly on account of the complexity of the involved geometries combined with nonlinear transport interactions. In the present study, a novel one-field modeling approach for multiscale fluid–solid interactions is proposed that does not need any a priori information on permeability. This approach implicitly considers the existence of multiscale structures through a penalization function that encompasses merely one single effective parameter. The definition, determination, as well as the response of the effective parameter to influencing factors are elaborated in detail. It is demonstrated that this approach is effective in representing properly the heterogeneity of solids. The method has been successfully applied to both nonlinear porous media flows and Darcian transport problems, exhibiting comparable accuracy but substantial computational savings as opposed to pore-scale simulations. It leads to more accurate interphase mass transfer predictions and lower computational cost in comparison with the Darcy–Brinkmann–Stokes approach. Overall, this method appears to be highly effective in forecasting realistic, industrial-scale porous media transport problems.

An accurate measurement method for serum homocysteine measurement by ID-LC/MS/MS and the application of external quality assessment

BackgroundSerum homocysteine (Hcy) measurement accuracy is essential for detecting and diagnosing cardio-cerebrovascular illnesses. Although many different methods have been developed to determine the concentration of Hcy, those different assays showed nonequivalent results. This study aimed to develop an accurate and precise isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC/MS/MS) method for serum homocysteine (Hcy) and assign values for reference materials used in external quality assessment (EQA) programs. MethodsDifferent concentrations of homocysteine calibration solutions were prepared with d4-Hcy as the internal standard. This method employed DTT to reduce protein-bound Hcy, followed by protein precipitation, and gradient elution on a Supelcosil LC-CN column for chromatographic separation, and multiple reaction monitor (MRM) mode with electrospray ionization (ESI) for mass spectrometric detection. After optimized ID-LC/MS/MS parameters, imprecision, trueness, the limit of quantification (LoQ), the limit of detection (LoD), and measurement uncertainty were evaluated to check the methodological performance. The established method was employed in assigning values to EQA samples, which were sent to 63 clinical laboratories in Beijing to measure Hcy. ResultsAt 10.69,15.99, and 37.80 μmol/L levels, the present method demonstrated analytical imprecision of 0.57 %, 0.65 %, and 0.57 %, and recoveries of 99.67 % to 100.21 %, respectively. The bias between the target values of GBW (Guojia Biaozhun Wuzhi) were − 0.79 % to 0.62 %. The LoQ and LoD for Hcy were 0.36 nmol/L and 0.27 nmol/L. The method had an uncertainty (U 95 %) of 1.34 % to 1.48 %. For the three levels of EQA samples, the percentage of laboratories meeting the trueness evaluation criteria (±10 %) was 81.67 %, 83.33 %, and 71.67 % respectively. ConclusionsWith optimal method precision and trueness, the ID-LC/MS/MS method to measure serum Hcy can be used for value assignment of EQA samples, which can provide reliable data for monitoring the accuracy of clinical laboratory for Hcy measurement.

Simultaneous Analysis of 504 Pesticide Multiresidues in Crops Using UHPLC-QTOF at MS1 and MS2 Levels.

A robust analytical method was developed for the simultaneous detection of 504 pesticide multiresidues in various crops using ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF). The method integrates both MS1 and MS2 levels through sequential window acquisition of all theoretical mass spectra (SWATH) analysis, allowing for accurate mass measurements and the construction of a spectral library to enhance pesticide residue identification. An evaluation of the method was carried out according to international standards, including the FAO guidelines and SANTE/11312/2021. Validation across five representative crops-potato, cabbage, mandarin, brown rice, and soybean-demonstrated exceptional sensitivity, with over 80% of the analytes detected at trace levels (≤2.5 μg/kg). Moreover, an impressive 96.8% to 98.8% of the compounds demonstrated LOQs of ≤10 μg/kg. Most compounds exhibited excellent linearity (r2 ≥ 0.980) and satisfactory recovery rates at spiking levels of 0.01 and 0.1 mg/kg. Among 42 crop samples analyzed, pesticides were detected in 1 cabbage, 3 mandarin, and 6 rice samples, with a mass accuracy within ±5 ppm and a Fit score ≥ 70.8, confirming the method's practical applicability and reliability. The detected residues ranged from 12.3 to 339.3 μg/kg, all below the established maximum residue limits (MRLs). This comprehensive approach offers an efficient, reliable, and scalable solution for pesticide multiresidue monitoring, supporting food safety programs and regulatory compliance.

Multi-attribute method analysis of therapeutic monoclonal antibodies using an automated sample preparation system

The multi-attribute method (MAM) has attracted increased attention as an alternative strategy for evaluating structural heterogeneity using conventional separation techniques such as ion-exchange chromatography and capillary electrophoresis of therapeutic monoclonal antibodies (mAbs). One of the remaining challenges for the practical use of the MAM is reliable and robust continuous monitoring. In this study, we successfully established an automated sample preparation system as a solution to this issue. Through method optimization, we confirmed that the peptide purification step using a solid-phase extraction column, which is usually performed after the digestion step, was not mandatory and that the addition of methionine as an oxidation inhibitor was able to significantly reduce artificial oxidation. Importantly, the use of our system enabled high-precision analysis for targeted peptide monitoring without relying on the operator’s knowledge and experience with peptide mapping using liquid chromatography/mass spectrometry (LC/MS). Our system could also be useful as a platform approach for targeted peptide monitoring in MAM workflow of traditional IgG-type mAbs. Furthermore, using common samples that were prepared using the automated system, we assessed the compatibility of LC/MS system in the targeted peptide monitoring via a collaborative study with MS vendors. The results showed that there was no significant difference in the mass accuracy, repeatability of the peak retention time and variations of intermediate precision of the measurement values among the four LC/MS systems, suggesting sufficient compatibility among the LC/MS systems. MAM system using our automated sample preparation method, which had high intermediate precision, will be useful for release and stability testing as well as characterization and manufacturing process development.

Simultaneous metabolomics and lipidomics analysis based on 4in1 online analysis system reveal metabolic signatures in atherosclerotic mice

Developing efficient and comprehensive analysis methods for metabolomics and lipidomics in the biological tissues and body fluids is essential for understanding the disease mechanisms. Although various two-dimensional liquid chromatography-mass spectrometry (2D-LC-MS) methods have been proposed to expand metabolite coverage, achieving higher efficiency in integrated metabolomics and lipidomics studies remains a technical challenge. In this work, a novel 4in1 online analysis system with excellent reproducibility and mass accuracy was constructed for metabolomics and lipidomics study in various biological samples from atherosclerotic mice. This system enabled the simultaneous detection in both positive and negative ion modes with extensive polarity separation in a single analytical run. Using the 4in1 online analysis system, we identified distinct but complementary metabolic signatures associated with atherosclerosis in different biological samples. Specifically, a total of 230 and 170 differential metabolites or lipids were detected in mice plasma samples and aortic tissue samples, respectively, including glycerophospholipids, sphingolipids, fatty acyls, glycerolipids, carboxylic acids, and pyrimidine nucleosides. Additionally, atherosclerosis-related metabolic pathways involved in biosynthesis of unsaturated fatty acids, sphingolipid metabolism, cholesterol metabolism, glycerophospholipid metabolism, and choline metabolism further revealed. These findings demonstrate that the novel 4in1 online analysis system is a faithful, stable and powerful tool for comprehensive metabolomics and lipidomics studies in complex biological matrices.

Rapid QC-MS: Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control.

Consistently collecting high-quality liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) data is a time-consuming hurdle for untargeted workflows. Analytical controls such as internal and biological standards are commonly included in high-throughput workflows, helping researchers recognize low-integrity specimens regardless of their biological source. However, evaluating these standards as data are collected has remained a considerable bottleneck─in both person-hours and accuracy. Here we present Rapid QC-MS, an automated, interactive dashboard for assessing LC-MS/MS data quality. Minutes after a new data file is written, a browser-viewable dashboard is updated with quality control results spanning multiple performance dimensions such as instrument sensitivity, in-run retention time shifts, and mass accuracy drift. Rapid QC-MS provides interactive visualizations that help users recognize acute deviations in these performance metrics, as well as gradual drifts over periods of hours, days, months, or years. Rapid QC-MS is open-source, simple to install, and highly configurable. By integrating open-source Python libraries and widely used MS analysis software, it can adapt to any LC-MS/MS workflow. Rapid QC-MS runs locally and offers optional remote quality control by syncing with Google Drive. Furthermore, Rapid QC-MS can operate in a semiautonomous fashion, alerting users to specimens with potentially poor analytical integrity via frequently used messaging applications. Initially developed for integration with Thermo Orbitrap workflows, Rapid QC-MS offers a fast, straightforward approach to help users collect high-quality untargeted LC-MS/MS data by eliminating many of the most time-consuming steps in manual data curation. Download for free: https://github.com/czbiohub-sf/Rapid-QC-MS.

Identification of Endosonographic Features that Compromise EUS-FNB Diagnostic Accuracy in Pancreatic Masses.

Endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) is highly accurate for diagnosing pancreatic mass. However, making diagnosis is challenging in 5-20% of patients. This study investigated the challenging features associated with reduced diagnostic performance in EUS-FNB and potential rescue methods that can improve the diagnostic rate. This single-center retrospective study included patients with solid pancreatic tumors who underwent EUS-FNB between January 1, 2019, and December 12, 2021. Patients without a computed tomography (CT) scan or definite diagnosis were excluded. Challenging features were features that reduced diagnostic accuracy in EUS-FNB, as determined through multivariate analysis. Rescue methods were methods that assisted operators in assessing lesions in patients with challenging features. Of 332 enrolled patients, an accurate diagnosis obtained using EUS-FNB was achieved in 286 (86.1%). Univariable analysis revealed that the diagnostic accuracy was lower in cases of pancreatic tumors with isoattenuation in CT images (77.3% vs. 89.8%, odds ratio [OR]: 0.39, p = 0.003), an ill-defined margin on EUS (61.2% vs. 92.5%, OR: 0.13, p < 0.001), or tumor size < 20mm (65.5% vs. 88.1%, OR: 0.26, p = 0.002). However, only ill-defined margins on EUS (OR: 0.14, p < 0.001) and tumor size < 20mm (OR: 0.25, p = 0.005) were independent predictors of inconclusive EUS-FNB in the multivariate analysis. The use of contrast (OR: 4.46, p = 0.026) and a highly experienced endosonographer (> 5cases/month; OR: 3.25, p = 0.034) improved diagnostic performance in difficult cases. Pancreatic tumors with ill-defined tumor margins on EUS or size < 20mm are challenging features in EUS-FNB. The use of contrast and a highly experienced endosonographer can improve diagnostic performance in difficult cases.

CHEX-MATE: Dynamical masses for a sample of 101 Planck Sunyaev-Zeldovich-selected galaxy clusters

The Cluster HEritage project with XMM-Newton – Mass Assembly and Thermodynamics at the Endpoint of structure formation (CHEX-MATE) is a programme to study a minimally biased sample of 118 galaxy clusters detected by Planck through the Sunyaev–Zeldovich effect. Accurate and precise mass measurements are required to exploit CHEX-MATE as an astrophysical laboratory and a calibration sample for cosmological probes in the era of large surveys. We measured masses based on the galaxy dynamics, which are highly complementary to weak-lensing or X-ray estimates. We analysed the sample with a uniform pipeline that is stable both for poorly sampled or rich clusters ---using spectroscopic redshifts from public (NED, SDSS, and DESI) or private archives--- and dedicated observational programmes. We modelled the halo mass density and the anisotropy profile. Membership is confirmed with a cleaning procedure in phase space. We derived masses from measured velocity dispersions under the assumed model. We measured dynamical masses for 101 CHEX-MATE clusters with at least ten confirmed members within the virial radius $r_ 200c $. Estimated redshifts and velocity dispersions agree with literature values when available. Validation with weak-lensing masses shows agreement within $8 (stat.) (sys.) \,&lt;!PCT!&gt;$, and confirms dynamical masses as an unbiased proxy. Comparison with Planck masses shows them to be biased low by $34 (stat.) (sys.) \,&lt;!PCT!&gt;$. A follow-up spectroscopic campaign is underway to cover the full CHEX-MATE sample.

Identification of novel microcystins in algal extracts by a liquid chromatography–high-resolution mass spectrometry data analysis pipeline

BackgroundMicrocystins are an emergent public health problem. These toxins are secondary metabolites of harmful cyanobacterial blooms, with blooms becoming more prevalent with eutrophication of water. Exposure to microcystins can result in sickness, liver damage, and even death. Over 300 microcystins have been identified to date, with differences in toxicity based on the specific amino acid composition. Because of this diversity in microcystins, as well as the likelihood of detecting as yet undiscovered microcystins, it is vital to establish a methodological workflow to identify any microcystin in a complex sample, regardless of the availability of a reference standard. Additionally, ascribing varying levels of confidence to these identifications is critical to effectively communicate discoveries. MethodsA liquid-chromatography–high-resolution mass spectrometry method was utilized to identify microcystins present in cyanobacterial extracts from a strain of Microcystis aeruginosa and an Aphanizomenon sp. First, microcystin congeners with available standards were identified in the cyanobacterial extract. These known-unknown microcystins were considered to have the highest confidence identifications due to availability of accurate masses, retention times, and library spectra for comparison. Utilizing the spectra of these microcystins, relatively high-abundance diagnostic product-ions were identified and employed to screen the data for additional candidate microcystins. Microcystins without a standard that had an exact mass matching a microcystin published in CyanoMetDB were considered semi-known-unknown microcystins. The remaining microcystins were considered unknown-unknown microcystins. The identities of the microcystins determined herein were additionally supported by product-ion analysis, thiol reactivity, esterification reactions, neutral loss analysis, and literature contextualization. ResultsIn total, utilizing the systematic workflow presented herein, 23 microcystins were identified in the M. aeruginosa culture, including two not published previously: [d-Asp3]MC-LCit and the incompletely identified MC-L(C7H11NO3).