scholarly journals GlycanGUI: Automated Glycan Annotation and Quantification Using Glucose Unit Index

2021 ◽  
Vol 9 ◽  
Author(s):  
Rui Zhang ◽  
Wenjing Peng ◽  
Sakshi Gautam ◽  
Yifan Huang ◽  
Yehia Mechref ◽  
...  
Keyword(s):  
Experimental Data ◽  
Retention Time ◽  
Laboratory Data ◽  
Internal Standard ◽  
Software Tool ◽  
Graphic User Interface ◽  
Liquid Chromatography Mass Spectrometry ◽  
Experimental Conditions ◽  
Glucose Unit ◽  
Unit Index

The retention time provides critical information for glycan annotation and quantification from the Liquid Chromatography Mass Spectrometry (LC-MS) data. However, the variation of the precise retention time of glycans is highly dependent on the experimental conditions such as the specific separating columns, MS instruments and/or the buffer used. This variation hampers the exploitation of retention time for the glycan annotation from LC-MS data, especially when inter-laboratory data are compared. To incorporate the retention time of glycan across experiments, Glucose Unit Index (GUI) can be computed using the dextrin ladder as internal standard. The retention time of glycans are then calibrated with respect to glucose units derived from dextrin ladders. Despite the successful application of the GUI approach, the manual calibration process is quite tedious and often error prone. In this work, we present a standalone software tool GlycanGUI, with a graphic user interface to automatically carry out the GUI-based glycan annotation/quantification and subsequent data analysis. When tested on experimental data, GlycanGUI reported accurate GUI values compared with manual calibration, and thus is ready to be used for automated glycan annotation and quantification using GUI.

scholarly journals New correlations for predicting two-phase electrical submersible pump performance under downhole conditions using field data

2021 ◽  
Author(s):  
Thuy Chu ◽  
Tan C. Nguyen ◽  
Jihoon Wang ◽  
Duc Vuong
Keyword(s):  
Experimental Data ◽  
Field Data ◽  
Laboratory Data ◽  
Performance Curve ◽  
Submersible Pump ◽  
Two Phase ◽  
Experimental Conditions ◽  
Pump Performance ◽  
Free Gas ◽  
Electrical Submersible Pump

AbstractElectrical Submersible Pump (ESP) is one of the major Artificial Lift methods that is reliable and effective for pumping high volume of fluids from wellbores. However, ESP is not recommended for applications with high gas liquid ratio. The presence of free gas inside the pump causes pump performance degradation which may lead to problems or even failure during operations. Thus, it is important to investigate effect of free gas on ESP performance under downhole conditions. At present, existing models or correlations are based on/verified with experimental data. This study is one of the first attempts to develop correlations for predicting two-phase gas–liquid pump performance under downhole conditions by using field data and laboratory data. Field data from three oil producing wells provided by Strata Production Company and Perdure Petroleum LLC. as well as experimental data obtained from experimental facility at Production and Drilling Research Project—New Mexico Tech were used in this study. Actual two-phase pump differential pressure per stage is obtained from experiments or estimated from field data and was normalized using pump performance curve. The values are compared to pump performance curve to study the relationships between pump performance and free gas percentage at pump intake. Correlations to predict ESP performance in two-phase flow under downhole and experimental conditions was derived from the results using regression technique. The correlation developed from field data presented in this study can be used to predict two-phase ESP performance under downhole conditions and under high gas fraction. The results from the experimental data confirm the reliability of the developed correlation using field data to predict two-phase ESP performance under downhole conditions. The developed correlation using the laboratory data predicts quite well the two-phase pump performance at the gas fraction of less than 15% while it is no longer reliable when free gas fraction is more than 15%. The findings from this study will help operating companies as well as ESP manufacturers to operate ESPs within the recommended range under downhole conditions. However, it is recommended to use the proposed correlation on reservoirs with conditions similar to those of the three presented wells.

Utilization of a Dextran Ladder to Standardize PGC-LC-MS-Based Glycomics

2018 ◽  
Author(s):  
Christopher Ashwood ◽  
Brian Pratt ◽  
Brendan MacLean ◽  
Nicolle H. Packer
Keyword(s):  
Retention Time ◽  
Internal Standard ◽  
Automated Assignment ◽  
Glycan Structure ◽  
Spectral Library ◽  
Reference Library ◽  
Glucose Unit ◽  
Unit Value ◽  
Area Variation ◽  
Core Fucosylation

<p>Porous graphitised carbon (PGC) based chromatographic separation of glycans achieves high-resolution separation of glycan mixtures released from glycoproteins, including structurally similar isomers. While there is some understanding of glycan separation on PGC, system-independent retention values have not been established.</p> <p> </p> <p>Using hydrolysed dextran as an internal standard, and Skyline software for post-acquisition normalisation, retention time and glycan peak area variation of replicate injections of glycan mixtures was significantly reduced. Normalisation of retention time to the dextran ladder allowed assignment of system-independent retention values, values that are applicable to all PGC-based separations regardless of chromatographic system. We have built a library of over 300 PGC-separated glycan structures with assigned normalised glucose unit (GU) PGC retention values.</p> <p> </p> <p>To further define the mechanism of glycan separation with PGC, we identified predictive models for the chromatographic effects resulting from addition and/or removal of core-fucosylation and bisecting GlcNAc based on the PGC normalised retention time library. A dextran ladder spectral library was also built to ensure correct retention time assignment of the internal standard added to glycan mixtures. Using the spectral matching feature in Skyline, isomeric discrimination between <i>O</i>-mannosylated glycans and the glucose-based dextran ladder was achieved.</p> <p> </p> <p>As a result, system-independent automated assignment of glycan structure based on precursor mass and glucose unit value, using a glycan structure reference library, can be achieved using PGC-LC-MS. </p>

scholarly journals Glucose unit index (GUI) of permethylated glycans for effective identification of glycans and glycan isomers

The Analyst ◽  
2020 ◽  
Vol 145 (20) ◽  
pp. 6656-6667 ◽  
Author(s):  
Sakshi Gautam ◽  
Wenjing Peng ◽  
Byeong Gwan Cho ◽  
Yifan Huang ◽  
Alireza Banazadeh ◽  
...  
Keyword(s):  
Retention Time ◽  
Glucose Unit ◽  
P Retention ◽  
Unit Index

Retention time normalization of permethylated glycans and glycan isomers across different instruments and laboratories, using standard dextrin ladder. (Figure created with BioRender.com).

Bioanalytical method development and validation of simultaneous analysis of telmisartan and hydrochlorthiazide in human plasma using LC-MS/MS

2016 ◽  
Vol 5 (03) ◽  
pp. 4862 ◽  
Author(s):  
Mathew George* ◽  
Lincy Joseph ◽  
Arpit Kumar Jain ◽  
Anju V.
Keyword(s):  
Human Plasma ◽  
Retention Time ◽  
High Performance ◽  
Method Development ◽  
Matrix Effects ◽  
Solid Phase ◽  
Internal Standard ◽  
Assay Method ◽  
Buffer System ◽  
Internal Standards

A simple, sensitive, rapid and economic high performance thin layer chromatographic method and a mass spectroscopic assay method has been developed for the quantification of telmisartan and hydrochlorthiazide combination in human plasma. The internal standards and analytes were extracted from human plasma by solid-phase extraction with HLB Oasis1cc (30mg) catridges. The scanning and optimization for the samples are done using methanol: water (50:50). The samples were chromatographed using reverse phase chromatography with C-18 column of different manufacturers like Ascentis C18 (150×4. 6, 5µ) using the buffer system Acetonitrile: Buffer (80:20%v/v) which consist of 2±0. 1Mm ammonium format at a flow rate of 0. 7ml/min at a column oven temperature 35±10c. The internal standard used was hydrochlorthiazide13c1, d2 and telmisartand3. The extraction techniques include conditioning, loading, washing and elution, drying followed by reconstitution of the dried samples. The volume injected was 10µl with the retention time of 3-4 min for telmisartan, 1-2 min for hydrochlorthiazide and for the internal standards the retention time was 3-4 min for telmisartand3 and 1-2 min for hydrochlorthiazide c13d2. The rinsing solution was Acetonitrile: HPLC grade water in the ratio (50:50). The above developed method was validated using various parameters like selectivity and sensitivity, accuracy and precision, matrix effects, % recovery and various stability studies. The method was proved to be sensitive, accurate, precise and reproducible. The preparation showed high recovery for the quantitative determination of telmisartan and hydrochlorthiazide in human plasma.

Determination of alcohols in mixtures by 19F NMR spectroscopy using hexefluoroacetone reagent

1982 ◽  
Vol 47 (7) ◽  
pp. 1973-1978 ◽  
Author(s):  
Jiří Karhan ◽  
Zbyněk Ksandr ◽  
Jiřina Vlková ◽  
Věra Špatná
Keyword(s):  
Standard Deviation ◽  
Nmr Spectroscopy ◽  
Standard Method ◽  
Internal Standard ◽  
Internal Standard Method ◽  
Concentration Region ◽  
Experimental Conditions ◽  
Curve Method ◽  
Sample Preparation Procedure

The determination of alcohols by 19F NMR spectroscopy making use of their reaction with hexafluoroacetone giving rise to hemiacetals was studied on butanols. The calibration curve method and the internal standard method were used and the results were mutually compared. The effects of some experimental conditions, viz. the sample preparation procedure, concentration, spectrometer setting, and electronic integration, were investigated; the conditions, particularly the concentrations, proved to have a statistically significant effect on the results of determination. For the internal standard method, the standard deviation was 0.061 in the concentration region 0.032-0.74 mol l-1. The method was applied to a determination of alcohols in the distillation residue from an oxo synthesis.

scholarly journals Zeolite NaP1 Functionalization for the Sorption of Metal Complexes with Biodegradable N-(1,2-dicarboxyethyl)-D,L-aspartic Acid

Materials ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2518
Author(s):  
Dorota Kołodyńska ◽  
Yongming Ju ◽  
Małgorzata Franus ◽  
Wojciech Franus
Keyword(s):  
Experimental Data ◽  
Aspartic Acid ◽  
Ph Value ◽  
Complexing Agents ◽  
X Ray Diffraction ◽  
Experimental Conditions ◽  
Modified Zeolite ◽  
X Ray ◽  
Slow Release Fertilizers ◽  
Pseudo Second Order

The possibility of application of chitosan-modified zeolite as sorbent for Cu(II), Zn(II), Mn(II), and Fe(III) ions and their mixtures in the presence of N-(1,2-dicarboxyethyl)-D,L-aspartic acid, IDHA) under different experimental conditions were investigated. Chitosan-modified zeolite belongs to the group of biodegradable complexing agents used in fertilizer production. NaP1CS as a carrier forms a barrier to the spontaneous release of the fertilizer into soil. The obtained materials were characterized by Fourier transform infrared spectroscopy (FTIR); surface area determination (ASAP); scanning electron microscopy (SEM-EDS); X-ray fluorescence (XRF); X-ray diffraction (XRD); and carbon, hydrogen, and nitrogen (CHN), as well as thermogravimetric (TGA) methods. The concentrations of Cu(II), Zn(II), Mn(II), and Fe(III) complexes with IDHA varied from 5–20 mg/dm3 for Cu(II), 10–40 mg/dm3 for Fe(III), 20–80 mg/dm3 for Mn(II), and 10–40 mg/dm3 for Zn(II), respectively; pH value (3–6), time (1–120 min), and temperature (293–333 K) on the sorption efficiency were tested. The Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin adsorption models were applied to describe experimental data. The pH 5 proved to be appropriate for adsorption. The pseudo-second order and Langmuir models were consistent with the experimental data. The thermodynamic parameters indicate that adsorption is spontaneous and endothermic. The highest desorption percentage was achieved using the HCl solution, therefore, proving that method can be used to design slow-release fertilizers.

SIMULTANEOUS ESTIMATION OF CURCUMIN AND GEFITINIB IN BULK AND TISSUE SAMPLES (PLASMA AND BRAIN HOMOGENATE) BY RP-HPLC: APPLICATION TO A DISTRIBUTION STUDY

INDIAN DRUGS ◽  
2019 ◽  
Vol 56 (07) ◽  
pp. 59-68
Author(s):  
H Mahajan ◽  
S Savale ◽  
P Nerkar ◽  
Keyword(s):  
Flow Rate ◽  
Mobile Phase ◽  
Internal Standard ◽  
Brain Homogenate ◽  
Reversed Phase ◽  
Hplc Method ◽  
Simultaneous Estimation ◽  
Bulk Analysis ◽  
Experimental Conditions ◽  
Rp Hplc

The present study was aimed at developing a Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) method for simultaneous determination of curcumin (CRM) and gefitinib (GFT) in bulk, plasma and brain homogenate. hydrochlorothiazide was used as an internal standard (IS). A new simple, rapid, selective, precise and accurate RP-HPLC method has been developed. The separation was achieved by using C-18 column (Qualisil BDS C18, 250 mm x 4.6 mm I.D.) coupled with a guard column of silica, mobile phase consisted of acetonitrile: water with 0.1% formic acid (30:70 v/v). The flow rate was 0.2 ml/min and the drug was detected using PDA detector at the wavelength of 242 nm. The experimental conditions, including the diluting solvent, mobile phase composition, column saturation and flow rate, were optimised to provide high-resolution and reproducible peaks. The method was developed and tested for linearity range of 10-60 μg/mL for bulk analysis and 200-800 ng/mL for plasma and brain homogenate. The developed method was validated as per ICH guidelines, in terms of linearity, application of the proposed method to bulk sample, recovery, precision, repeatability, ruggedness, sensitivity (LOD and LOQ) and robustness and stability study (short and long-term stabilities, freeze/thaw stability, post-preparative). The low value of % RSD showed that the method was precise within the acceptance limit of 2%. The developed method was successfully applied for the analysis of the drug in bulk as well as various marketed formulation and drug in plasma and brain distribution studies.

scholarly journals NEW METHOD DEVELOPMENT AND VALIDATION FOR THE DETERMINATION OF FEBUXOSTAT IN HUMAN PLASMA BY LIQUID CHROMATOGRAPHY–MASS SPECTROMETRY

2016 ◽  
Vol 8 (9) ◽  
pp. 61 ◽  
Author(s):  
Narottam Pal ◽  
Avanapu Srinivasa Rao ◽  
Pigilli Ravikumar
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Human Plasma ◽  
Method Development ◽  
Multiple Reaction Monitoring ◽  
Internal Standard ◽  
New Method ◽  
Liquid Chromatography Mass Spectrometry ◽  
Chromatography Mass Spectrometry

<p><strong>Objective</strong>:<strong> </strong>To develop a new method and validate the same for the determination of Febuxostat (FBS) in human plasma by liquid chromatography–mass spectrometry (LCMS).</p><p><strong>Methods</strong>:<strong> </strong>The present method utilized reversed-phase high-performance liquid chromatography with tandem mass spectroscopy. Febuxostat D9 (FBS D9) was used as internal standard (IS). The analyte and internal standard were separated from human plasma by using solid phase extraction method. Zorbax Eclipse XDB, C<sub>8</sub>, 100 mm x 4.6 mm, 3.5 µm column was used and HPLC grade acetonitrile, 5 millimolar (mM) ammonium format (80: 20, v/v) as mobile phase, detected by mass spectrometry operating in positive ion and multiple reaction monitoring modes.</p><p><strong>Results</strong>:<strong> </strong>The parent and production transitions for FBS and internal standard were at m/z 317.1→261.0 and 326.1→262.0 respectively. The method was validated for system suitability, specificity, carryover effect, linearity, precision, accuracy, matrix effect, sensitivity and stability. The linearity range was from 20.131 ng/ml to10015. 534 ng/ml with a correlation coefficient of 0.999. Precision results (%CV) across six quality control samples were within the limit. The percentage recovery of FBS and internal standard from matrix samples was found to be 76.57% and 75.03% respectively.</p><p><strong>Conclusion</strong>:<strong> </strong>Present study describes new LC-MS method for the quantification of FBS in a pharmaceutical formulation. According to validation results, it was found to be a simple, sensitive, accurate and precise method and also free from any kind of interference. Therefore the proposed analytical method can be used for routine analysis for the estimation of FBS in its formulation.</p>

Sign in / Sign up

Export Citation Format

Share Document