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).

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.

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>

Impact of Metal Pad Etch-Induced Plasma Damage on Dynamic Retention Time Degradation during High Temperature Stress in High Density DRAM Technology

2005 ◽  
Author(s):  
D-J Kim ◽  
I-G Kim ◽  
J-Y Noh ◽  
H-J Lee ◽  
S-H Park ◽  
...  
Keyword(s):  
High Temperature ◽  
Temperature Stress ◽  
Retention Time ◽  
High Temperature Stress ◽  
High Density ◽  
Cell Junction ◽  
Antenna Effect ◽  
Plasma Damage ◽  
Root Cause ◽  
Wafer Processing

Abstract As DRAM technology extends into 12-inch diameter wafer processing, plasma-induced wafer charging is a serious problem in DRAM volume manufacture. There are currently no comprehensive reports on the potential impact of plasma damage on high density DRAM reliability. In this paper, the possible effects of floating potential at the source/drain junction of cell transistor during high-field charge injection are reported, and regarded as high-priority issues to further understand charging damage during the metal pad etching. The degradation of block edge dynamic retention time during high temperature stress, not consistent with typical reliability degradation model, is analyzed. Additionally, in order to meet the satisfactory reliability level in volume manufacture of high density DRAM technology, the paper provides the guidelines with respect to plasma damage. Unlike conventional model as gate antenna effect, the cell junction damage by the exposure of dummy BL pad to plasma, was revealed as root cause.

Studies on Chromatographic Fractioning by Cations Exchangers of a Bovine Hemoglobin Hydrolysate

2018 ◽  
Vol 69 (10) ◽  
pp. 2794-2798
Author(s):  
Alina Diana Panainte ◽  
Ionela Daniela Morariu ◽  
Nela Bibire ◽  
Madalina Vieriu ◽  
Gladiola Tantaru ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Retention Time ◽  
Chromatographic Separation ◽  
Bovine Hemoglobin ◽  
Reverse Phase ◽  
Hplc System ◽  
Fast Flow ◽  
Hydrolysis Of ◽  
Phase Column

A peptidic hydrolysate has been obtained through hydrolysis of bovine hemoglobin using pepsin. The fractioning of the hydrolysate was performed on a column packed with CM-Sepharose Fast Flow. The hydrolysate and each fraction was filtered and then injected into a HPLC system equipped with a Vydak C4 reverse phase column (0.46 x 25 cm), suitable for the chromatographic separation of large peptides with 20 to 30 amino acids. The detection was done using mass spectrometry, and the retention time, size and distribution of the peptides were determined.

Deep Shaft High Rate Aerobic Digestion: Laboratory and Pilot Plant Performance

1981 ◽  
Vol 16 (1) ◽  
pp. 71-90 ◽  
Author(s):  
F. Tran ◽  
D. Gannon
Keyword(s):  
Retention Time ◽  
Oxygen Transfer ◽  
Pilot Plant ◽  
High Rate ◽  
Plant Performance ◽  
High Solids ◽  
Aerobic Digestion ◽  
Volatile Solids ◽  
Solids Content ◽  
High Solids Content

Abstract The Deep Shaft process, originating from ICI Ltd. in the U.K., has been further developed by C-I-L Inc., Eco-Technology Division into an extremely energy efficient, high rate biological treatment process for industrial and municipal wastewaters. The Deep Shaft is essentially an air-lift reactor, sunk deep in the ground (100 - 160 m): the resulting high hydrostatic pressure together with very efficient mixing in the shaft provide extremely high oxygen transfer efficiencies (O.T.E.) of up to 90% vs 4 to 20% in other aerators. This high O.T.E. suggests real potential for Deep Shaft technology in the aerobic digestion of sludges and animal wastes: with conventional aerobic digesters an O.T.E. over 8% is extremely difficult to achieve. This paper describes laboratory and pilot plant Deep Shaft aerobic digester (DSAD) studies carried out at Eco-Research's Pointe Claire, Quebec laboratories, and at the Paris, Ontario pilot Deep Shaft digester. An economic pre-evaluation indicated that DSAD had the greatest potential for treating high solids content primary or secondary sludge (3-7% total solids) in the high mesophilic and thermophilic temperature range (25-60°C) i.e. in cases where conventional digesters would experience severe limitations of oxygen transfer. Laboratory and pilot plant studies have accordingly concentrated on high solids content sludge digestion as a function of temperature. Laboratory scale daily draw and fill DSAD runs with a 5% solids sludge at 33°C with a 3 day retention time have achieved 34% volatile solids reduction and a stabilized sludge exhibiting a specific oxygen uptake rate (S.O.U.R.) of less than 1 mgO2/gVSS/hour, measured at 20°C. This digestion rate is about four times faster than the best conventional digesters. Using Eco-Research's Paris, Ontario pilot scale DSAD (a 160 m deep 8 cm diameter u-tube), a 40% reduction in total volatile solids, (or 73% reduction of biodegradable VS) and a final SOUR of 1.2 mg02/gVSS/hour have been achieved for a 4.6% solids sludge in 4 days at 33°C, with loading rates of up to 7.9 kg VSS/m3-day. Laboratory runs at thermophilic temperatures (up to 60°C) have demonstrated that a stabilized sludge (24-41% VSS reduction) can be produced in retention time of 2 days or less, with a resulting loading rate exceeding 10 kg VSS/m3-day.

The Impact of a Chemostat Discharge Containing Oil Degrading Bacteria on the Biological Kinetics of a Refinery Activated Sludge Process

1988 ◽  
Vol 20 (11-12) ◽  
pp. 131-136 ◽  
Author(s):  
A. D. Wong ◽  
C. D. Goldsmith
Keyword(s):  
Activated Sludge ◽  
Retention Time ◽  
Waste Treatment ◽  
Treatment Plant ◽  
Utilization Rate ◽  
Activated Sludge Process ◽  
Kinetic Evaluation ◽  
Degrading Bacteria ◽  
Waste Treatment Plant ◽  
The Impact

The effect of discharging specific oil degrading bacteria from a chemostat to a refinery activated sludge process was determined biokinetically. Plant data for the kinetic evaluation of the waste treatment plant was collected before and during treatment. During treatment, the 500 gallon chemostatic growth chamber was operated on an eight hour hydraulic retention time, at a neutral pH, and was fed a mixture of refinery wastewater and simple sugars. The biokinetic constants k (days−1), Ks (mg/L), and K (L/mg-day) were determined before and after treatment by Monod and Lineweaver-Burk plots. Solids discharged and effluent organic concentrations were also evaluated against the mean cell retention time (MCRT). The maximum utilization rate, k, was found to increase from 0.47 to 0.95 days−1 during the operation of the chemostat. Subsequently, Ks increased from 141 to 556 mg/L. Effluent solids were shown to increase slightly with treatment. However, this was acceptable due to the polishing pond and the benefit of increased ability to accept shock loads of oily wastewater. The reason for the increased suspended solids in the effluent was most likely due to the continual addition of bacteria in exponential growth that were capable of responding to excess substrate. The effect of the chemostatic addition of specific microbial inocula to the refinery waste treatment plant has been to improve the overall organic removal capacity along with subsequent gains in plant stability.

The nitrogen removal potential of predenitrification systems in sensitive coastal areas

1995 ◽  
Vol 32 (7) ◽  
pp. 135-142
Author(s):  
E. Görgün ◽  
N. Artan ◽  
D. Orhon ◽  
R. Tasli
Keyword(s):  
Water Quality ◽  
Wastewater Treatment ◽  
Nitrogen Removal ◽  
Retention Time ◽  
Treatment Process ◽  
Hydraulic Retention Time ◽  
Domestic Sewage ◽  
Coastal Areas ◽  
Careful Evaluation ◽  
Denitrification Kinetics

Effective nitrogen removal is now required to protect water quality in sensitive coastal areas. This involves a much more difficult treatment process than for conventional domestic sewage as wastewater quantity and quality exhibits severe fluctuations in touristic zones. Activated sludge is currently the most widely used wastewater treatment and may be upgraded as a predenitrification system for nitrogen removal. Interpretation of nitrification and denitrification kinetics reveal a number of useful correlations between significant parameters such as sludge age, C/N ratio, hydraulic retention time, total influent COD. Nitrogen removal potential of predenitrification may be optimized by careful evaluation of wastewater character and the kinetic correlations.

Effect of Physicochemical Variables on Algal Autoflotation

1992 ◽  
Vol 26 (7-8) ◽  
pp. 1769-1778 ◽  
Author(s):  
S.-I. Lee ◽  
B. Koopman ◽  
E. P. Lincoln
Keyword(s):  
Dissolved Oxygen ◽  
Oxygen Concentration ◽  
Retention Time ◽  
Contact Time ◽  
Pilot Scale ◽  
Dissolved Oxygen Concentration ◽  
Physicochemical Variables ◽  
Rise Rate ◽  
Mixing Intensity ◽  
Maximum Rise

Combined chemical flocculation and autoflotation were examined using pilot scale process with chitosan and alum as flocculants. Positive correlation was observed between dissolved oxygen concentration and rise rate. Rise rate depended entirely on the autoflotation parameters: mixing intensity, retention time, and flocculant contact time. Also, rise rate was influenced by the type of flocculant used. The maximum rise rate with alum was observed to be 70 m/h, whereas that with chitosan was approximately 420 m/h. The efficiency of the flocculation-autoflotation process was superior to that of the flocculation-sedimentation process.

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