Single-run Method Research Articles

Cross-Run Hybrid Features Improve the Identification of Data-Independent Acquisition Proteomics.

The analysis of data-independent acquisition (DIA) mass spectrometry data is crucial for comprehensive proteomics studies. However, traditional single-run methods often fall short in terms of identification depth and consistency. We present HFDiscrim, a specialized multirun DIA analysis tool aimed at enhancing the depth and consistency of reliable peptide identifications of DIA analysis tools. HFDiscrim was extensively benchmarked on multiple data sets, including the MCB data set, the ccRCC data set, and a three-species benchmark mixture. Compared to PyProphet, HFDiscrim identified 22.04% more precursors, 19.1% more peptides, and 13.2% more proteins while maintaining a controllable false discovery rate. Furthermore, HFDiscrim demonstrated higher identification rates and improved reproducibility across multiple runs. HFDiscrim is publicly available at https://github.com/yachliu/HFDiscrim.

Unified-Hydrophilic-Interaction/Anion-Exchange Liquid Chromatography Mass Spectrometry (Unified-HILIC/AEX/MS): A Single-Run Method for Comprehensive and Simultaneous Analysis of Polar Metabolome.

One of the technical challenges in the field of metabolomics is the development of a single-run method to detect the full complement of polar metabolites in biological samples. However, an ideal method to meet this demand has not yet been developed. Herein, we proposed a simple methodology that enables the comprehensive and simultaneous analysis of polar metabolites using unified-hydrophilic-interaction/anion-exchange liquid chromatography mass spectrometry (unified-HILIC/AEX/MS) with a polymer-based mixed amines column composed of methacrylate-based polymer particles with primary, secondary, tertiary, and quaternary amines as functional groups. The optimized unified-HILIC/AEX/MS method is composed of two consecutive chromatographic separations, HILIC-dominant separation for cationic, uncharged, and zwitterionic polar metabolites [retention times (RTs) = 0-12.8 min] and AEX-dominant separation for polar anionic metabolites (RTs = 12.8-26.5 min), by varying the ratio of acetonitrile to 40 mM ammonium bicarbonate solution (pH 9.8). A total of 400 polar metabolites were analyzed simultaneously through a combination of highly efficient separation using unified-HILIC/AEX and remarkably sensitive detection using multiple reaction monitoring-based triple quadrupole mass spectrometry (unified-HILIC/AEX/MS/MS). A nontargeted metabolomic approach using unified-HILIC/AEX high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) also provided more comprehensive information on polar metabolites (3242 metabolic features) in HeLa cell extracts than the conventional HILIC/HRMS method (2068 metabolic features). Our established unified-HILIC/AEX/MS/MS and unified-HILIC/AEX/HRMS methods have several advantages over conventional techniques, including polar metabolome coverage, throughput, and accurate quantitative performance, and represent potentially useful tools for in-depth studies on metabolism and biomarker discovery.

Facile preparation of hazy Ga-doped ZnO electrodes by atmospheric pressure plasma jet

Increasing the optical path length without degrading optoelectronic properties of front electrodes of solar cells is promising to enhance the power conversion efficiency. This can be achieved by increasing the haze (H) of the electrode through texturing, while retaining high transmittance (Tt) and low sheet resistance (Rs). However, it is challenging to balance these properties simultaneously since they are mutually influenced. Here, we present a facile, low-cost, and single-run method of preparing gallium-doped zinc oxide (GZO) with high H (>25%), high Tt (>90% in the visible range, referenced to glass), and low Rs (6.62 Ω sq−1) using atmospheric pressure plasma jet. First, we increase the nozzle-substrate distance, or working distance (WD), to deposit a thin, rough GZO as a haze enhance (HE) layer and immediately deposit a standard GZO layer using the same apparatus. By tailoring the roughness of the HE layer using WD and scanning pitch, we successfully produce high-quality hazy GZO that have competitive figures of merit of 6.3 × 10−2 Ω−1 (referenced to the glass) and 2.1 × 10−2 Ω−1 (overall), and H = 25%. Also, unlike conventional methods, our approach does not require vacuum, etching, additional materials, or change of machine/tooling, which can significantly reduce the operational complexity.

Development and validation of a single run method based on species specific isotope dilution and HPLC-ICP-MS for simultaneous species interconversion correction and speciation analysis of Cr(III)/Cr(VI) in meat and dairy products

This study presents the development, validation and application of a new analytical approach for the simultaneous speciation analysis of Cr(III) and Cr(VI) in meat and dairy products by high-performance liquid chromatography (HPLC) coupled to inductively coupled plasma mass spectrometry (ICP-MS) and double spike species specific-isotope dilution (SS-ID). The species extraction was achieved by sequential complexation of Cr(III) with ethylenediaminetetraacetic acid (EDTA) and of Cr(VI) with 1,5-diphenylcarbazide (DPC) in the same analytical run. The HPLC separation of complexed species was carried out using a short (5 cm) microbore anion-exchange HPLC column and a mobile phase consisting of 0.01 mol L−1 HNO3 + 2.5% (v/v) MeOH + 0.30 mol L−1 EDTA (pH = 2) in isocratic elution mode with excellent baseline separation achieved in less than 3 min. The method was validated by means of the accuracy profile approach by carrying out 6 measurement series in duplicate on (six) different days over a timespan of two months. The quantification limit was 0.013 μg kg−1 for Cr(III) and 0.049 μg kg−1 for Cr(VI), respectively. The measurement bias corresponding to the validity domain ranged from 0.01 to 0.11%, whereas the coefficient of variation in terms of repeatability (CVr) varied from 2.9 to 11.6% (depending on the analyte level) for Cr(III) and from 6.7 to 11.8% for Cr(VI). Similarly, the coefficient of variation in terms of intermediate reproducibility (CVR) ranged from 6.8 to 13% for Cr(III) and from 6.8 to 25.9% for Cr(VI), respectively. The method was successfully applied to the analysis of a selection of food samples such as baby and semi-skimmed milk and steak beef samples. Cr(VI) was not quantified in any of these samples while Cr(III) levels ranged between 2.7 and 4.7 μg kg−1, which were comparable with the levels of total chromium analysed in the same samples by ICP-MS (accredited method). The method presented here with combined use of species specific isotope dilution and sequential species complexation is a powerful analytical tool for accurate and precise quantification of Cr(III) and Cr(VI) at trace levels and allows for correction of any species interconversion during sample preparation.

System-based prediction of maneuvering performance of twin-propeller and twin-rudder ship using a modular mathematical model

The turning circle and zigzag maneuvering performance of surface combatant, DTMB 5415 have been investigated by using system-based method. Unsteady Reynolds averaged Navier Stokes (URANS) approach is utilized to estimate hydrodynamic derivatives and hull-propeller-rudder interactions. DTMB 5415 is a twin-propeller / twin-rudder ship and there are some studies on the derivation of maneuvering coefficients in the literature but none of them took into account the propeller and rudder forces. In this study, static drift, pure yaw, combined yaw and drift, self-propulsion and rudder tests of DTMB 5415 hull have been simulated in calm and deep water condition. Bare hull PMM simulations were carried out for a fixed Froude number of Fr=0.28, while the simulations related to rudder and propeller were performed at Fr=0.25. Computational results were used by MMG (Maneuvering Modeling Group) model to estimate the maneuvering performance of the ship. Hydrodynamic derivatives from numerically generated forces and moment data were obtained by single-run and multiple-run methods. The results from both methods were tested in an in-house maneuvering simulation code (MANSIM) that solves for ship motions and they were compared with computed turning circle and zigzag maneuvering performances. Although it is known a priori that the multiple-run method would give better solution in overall, it was found that the single-run method can be a good alternative in some specific cases. For the zigzag and turning circle tests, the results from single-run method were found satisfactory when correct PMM test conditions were adopted.

Screening of herbal medicines for potential allopathic antidiabetic adulterants: An analytical study.

Background:There are several reports worldwide on adulteration of herbal medicines (HMs) with allopathic drugs. In India, only a few studies have reported adulteration of HMs with antidiabetics and there are no systematic studies.Aims:To develop a rapid and validated method for detection of allopathic antidiabetic adulterants and to explore the extent of adulteration in HMs sold in South India.Materials and Methods:Standards and solvents were purchased from Sigma-Aldrich. Different brands of antidiabetic HM samples with manufacturing licenses were procured from dispensaries. Spiked drug free psyllium husk as solid and flask seed oil as liquid herbal matrices were used for method development. The spiked matrices with different concentrations were extracted with methanol and subjected to centrifugation. The supernatant was collected and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Isocratic elution was carried on a C18 column with 0.1% (v/v) formic acid:methanol (3:7, v/v) as a mobile phase. All drugs were monitored for two ion products in positive electrospray ionization mode using multiple reaction monitoring scans.Results:The retention time was 9 min. Limit of detection is 10 Pictograms (pg) for all analytes except for metformin, which was 370 pg. Recoveries of analytes range from 96% to 117%. Forty different brands of antidiabetic HMs were analyzed. Adulterant peaks were not observed in the mass chromatograms of HMs.Conclusions:A single-run method was developed by LC-MS/MS for the detection of proposed antidiabetics in HMs from licensed manufacturing units and online sold HMs across herbal dispensaries in Puducherry union territory, India. None of the HMs was found to be adulterated with proposed allopathic antidiabetic adulterants.

Force-velocity profiling of sprinting athletes: single-run vs. multiple-run methods.

This study explored the agreement between a single-run and a multiple-run method for force-velocity (Fv) profiling of sprinting athletes; we evaluated both absolute values and changes over time caused by sprint training. Seventeen female handball players (23 ± 3years, 177 ± 7cm, 73 ± 6kg) performed 30m un-resisted and resisted sprints (50, 80 and 110N resistance) before and after an 8-week sprint training intervention. Two approaches were used to calculate theoretical maximal velocity (v0), horizontal force (F0), power (Pmax), and the force-velocity slope (SFv): (1) the single-run method, based on inverse dynamics applied to the centre-of-mass movement, was calculated from anthropometric and sprint split time data; and (2) the multiple-run method, where peak velocity from un-resisted and resisted sprints were plotted against the horizontal resistances. Trivial differences in v0 (0.7%) were observed between the two calculation methods. Corresponding differences for F0, Pmax and SFv were 16.4, 15.6 and 17.6%, respectively (most likely; very large effect size). F0 showed poor agreement between the methods (r = 0.26 and 0.16 before and after the intervention). No substantial correlation between the changes (from pre- to post-training tests) in SFV calculated with the single-run and the multiple-run methods were observed (r = 0.03) [corrected]. This study revealed poor agreement between the Fv relationships of the investigated calculation methods. In practice, both methods may have a purpose, but the single-run and the multiple-run methods appear to measure somewhat different sprint properties and cannot be used interchangeably.

Stability Study of Etoricoxib a Selective Cyclooxygenase-2 Inhibitor by a New Single and Rapid Reversed Phase HPLC Method

Cyclooxygenase-2 (COX-2) is an enzyme responsible for inflammation and pain. Etoricoxib is the most recent selective (COX-2) inhibitor that has a higher COX-2 selectivity than the other COX-2-selective nonsteroidal anti-inflammatory drugs (NSAIDs), which significantly improves its gastric safety profile. The current therapeutic indications of etoricoxib includes the treatment of several painful conditions, such as osteoarthritis, acute gout, ankylosing spondylitis, and rheumatoid arthritis. To the best of found knowledge, no decent method has been reported that can be used for the routine determination of etoricoxib and additives in pharmaceutical suspensions by a single, rapid and cost-effective run of HPLC, using an UV-Vis detector. Earlier reported methods, such as liquid chromatography-mass spectrometry (LC-MS), high performance thin layer chromatography (HPTLC), capillary zone electrophoresis, and ultra performance liquid chromatography (UPLC), are all tedious and time consuming. A reversed phase high performance liquid chromatography (RP-HPLC) was used as a first reported single run method to achieve developed and validated simultaneous determination for sodium saccharin, vanillin, methyl paraben, etoricoxib, and butyl paraben, in prepared oral suspensions of etoricoxib. Reversed phase column of octadecylsilane (ODS) C18 with isocratic mobile phase containing methanol, and phosphate buffer of pH 6 in a ratio of 70:30 (v/v). Celecoxib is used as an internal standard at a detection wavelength of 215 nm. This method separates the analytes in a total running time less than 13 min. Linearity is obtained in the calibration curve for all analytes with a R2 value of > 0.999. Furthermore, beta-cyclodextrin (β-CD) and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) were added, either alone or combined, to prevent the crystal formation, and any unpleasant taste of etoricoxib in oral formulations. After testing both HP-β-CD and β-CD at 3% w/w for each, the results showed that HP-β-CD is more efficient in preventing the crystal formation of etoricoxib in suspensions at room temperature than β-CD is.

Opportunities and Constraints in Characterizing Landscape Distribution of an Invasive Grass from Very High Resolution Multi-Spectral Imagery.

Understanding spatial distributions of invasive plant species at early infestation stages is critical for assessing the dynamics and underlying factors of invasions. Recent progress in very high resolution remote sensing is facilitating this task by providing high spatial detail over whole-site extents that are prohibitive to comprehensive ground surveys. This study assessed the opportunities and constraints to characterize landscape distribution of the invasive grass medusahead (Elymus caput-medusae) in a ∼36.8 ha grassland in California, United States from 0.15m-resolution visible/near-infrared aerial imagery at the stage of late spring phenological contrast with dominant grasses. We compared several object-based unsupervised, single-run supervised and hierarchical approaches to classify medusahead using spectral, textural, and contextual variables. Fuzzy accuracy assessment indicated that 44–100% of test medusahead samples were matched by its classified extents from different methods, while 63–83% of test samples classified as medusahead had this class as an acceptable candidate. Main sources of error included spectral similarity between medusahead and other green species and mixing of medusahead with other vegetation at variable densities. Adding texture attributes to spectral variables increased the accuracy of most classification methods, corroborating the informative value of local patterns under limited spectral data. The highest accuracy across different metrics was shown by the supervised single-run support vector machine with seven vegetation classes and Bayesian algorithms with three vegetation classes; however, their medusahead allocations showed some “spillover” effects due to misclassifications with other green vegetation. This issue was addressed by more complex hierarchical approaches, though their final accuracy did not exceed the best single-run methods. However, the comparison of classified medusahead extents with field segments of its patches overlapping with survey transects indicated that most methods tended to miss and/or over-estimate the length of the smallest patches and under-estimate the largest ones due to classification errors. Overall, the study outcomes support the potential of cost-effective, very high-resolution sensing for the site-scale detection of infestation hotspots that can be customized to plant phenological schedules. However, more accurate medusahead patch delineation in mixed-cover grasslands would benefit from testing hyperspectral data and using our study’s framework to inform and constrain the candidate vegetation classes in heterogeneous locations.

Single-experiment input uncertainty

‘Input uncertainty’ refers to the simulation model risk caused by estimating input distributions from real-world data, and specifically the (usually unmeasured) variance in performance estimates that this introduces. We provide the first single-run method for quantifying input uncertainty, meaning that we derive our measure of input-uncertainty variance—both overall variance and the contribution to it of each input model—from the nominal experiment that the analyst would typically run using the estimated input models; other methods in the literature require additional diagnostic experiments. Application of our method is illustrated with two examples.

Optimizing discrete event dynamic systems via the gradient surface method

The authors propose a gradient surface method (GSM) for the optimization of discrete event dynamic systems. GSM combines the advantages of response surface methodology (RSM) and efficient derivative estimation techniques like perturbation analysis (PA) or the likelihood ratio (LR) method. In GSM, the gradient estimation is obtained by PA (or LR), and the performance gradient surface is obtained from observations at various points in a fashion similar to the RSM. Zero points of the successive approximating gradient surface are taken then as the estimates of the optimal solution. GSM is characterized by several attractive features: it is a single run method and more efficient than RSM; it uses at each iteration step the information from all data points rather than just the local gradient; and it tries to capture the global features of the gradient surface and thereby quickly arrives at the vicinity of the optimal solution. A number of examples are exhibited to illustrate this method. >

Simultaneous quantitation of quinidine, procainamide, and N-acetylprocainamide in serum by gas-liquid chromatography with a nitrogen-phosphorus selective detector.

We describe a single-run method for quantitating quinidine, procainamide, and N-acetylprocainamide, involving gas-liquid chromatography with a nitrogen-phosphorus selective detector. Within-run precision (CV) was 3% (x = 2 mg/L, n = 20), 6.9% (x = 4 mg/L, n = 10), and 1.5% (x = 8 mg/L, n = 8) for quinidine; 7.7% (x = 4 mg/L, n = 14), 1.6% (x = 8 mg/L, n = 16), and 2.3% (x = 12 mg/L, n = 12) for procainamide; and 6.3% (x = 5 mg/L, n = 6), 3.6% (x = 10 mg/L, n = 20), and 4.0% (x = 20 mg/L, n = 10) for N-acetylprocainamide.l Between-run precision was 3.0%(x = 2 mg/L, n = 20), 7.0% (x = 4 mg/L, n = 9), and 2.8% (x = 8 mg/L, n = 9) for quinidine; 4.7% (x = 4 mg/L, n = 10). 3.3% (x = 8 mg/L, n = 20), and 1.9% (x = 12 mg/L, n = 10) for procainamide; and 9.3% (x = 5 mg/L, n = 6), 4.3% (x = 10 mg/L, n = 20), and 3.8% (x = 20 mg/L, n = 10) for N-acetylprocainamide. Tube stoppers that contain a rubber plasticizer interfere with the technique. Clinical application and correlation with drug concentrations by this technique are discussed.