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Integrated Omics Technology for Basic and Clinical Research
Published in Jyoti Ranjan Rout, Rout George Kerry, Abinash Dutta, Biotechnological Advances for Microbiology, Molecular Biology, and Nanotechnology, 2022
Kuldeep Giri, Vinod Singh Bisht, Sudipa Maity, Kiran Ambatipudi
In today’s date, widely used methodologies to characterize peptides/ proteins are bottom-up and top-down approaches. In the bottom-up approach, which is more specific and sensitive, includes liquid chromatographic-based separation of peptides derived from enzymatic digestion (i.e., trypsin) of selected protein and their subsequent identification through MS. However, posttranslation modification such as glycosylation and phosphorylation is identified by performing a top-down approach that involves intact protein identification through the MS (Barbosa et al., 2012). Similarly, for labeled quantification of proteins, Isotope Coded Affinity Tag, is a sensitive technique used for relative quantitative analysis by tagging cysteine residues. Similarly, isobaric tags for relative and absolute quantification (iTRAQ) in protein extract and stable isotope labeling with amino acid in cell culture (SILAC) is used for quantitative comparison of experimentally tagged proteins to discriminate their abundances by MS in different samples (healthy vs. disease state) (Ong et al., 2002; Ross et al., 2004). High throughput MS technique such as MudPIT which is a two dimensional chromatography technique, using high-performance liquid chromatography (incorporate strong cation exchange and reversed-phase columns) coupled with tandem MS identification and quantifies protein from a complex mixture and determination of protein-protein interaction (Washburn et al., 2001). The label-free and labeled (SILAC and iTRAQ) approach for proteomes’ quantitation and subsequent analysis is represented in Figure 14.8.
Mobile Phase Effects in Reversed-Phase and Hydrophilic Interaction Liquid Chromatography
Published in Nelu Grinberg, Peter W. Carr, Advances in Chromatography Volume 57, 2020
Equation (1.17) is formally identical with the LSS gradient equation introduced by Snyder et al. [89], widely applied in RP systems. In some RP systems, the gradient elution volumes predicted from Equation (1.18), Equation (1.19) and Equation (1.20) provide comparable or even better agreement with the experimental data, for example, fast (1–2 min) gradients in the second dimension of comprehensive two-dimensional chromatography [107] using short packed [108], core-shell [109] or silica monolithic columns [110]. Figure 1.13 compares the prediction errors of the two-parameter displacement and LSS models and the three-parameter ABM model on short 5 cm C18 and Phenyl-Hexyl core-shell columns for 1–5 min acetonitrile-water gradients run at 2 mL/min and 4.5 ml/min [4]. The errors in the gradient retention volumes of alkylbenzenes and flavones predicted with the best-fit model parameters determined by the regression analysis of the isocratic and gradient input data decrease in the order: LSS > displacement > ABM models. The parameters of the ABM model acquired under gradient conditions provide prediction errors in the gradient elution volumes of alkylbenzenes (≤ 0.4% ) and flavones, (≤ 1.2%), in agreement with the results reported earlier [111]. The computation is relatively easy with the generally available statistical software. The strategy of the commercial DryLab gradient optimization software employs the LSS model and the experimental data acquired in two scouting gradient experiments [112,113].
Protein Expression Methods
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
MPLC and HPLC systems typically contain either two pumps that can be used for the creation of binary gradients or a low-pressure mixing valve that can be used to mix four to six solutions to create complex buffers (sometimes referred to as inline buffer preparation). Additionally, MPLC and HPLC systems can be configured with a variety of other detectors depending on the application, including conductivity meters and fluorescence detectors. Furthermore, some MPLC and HPLC systems incorporate valves that allow for two-dimensional chromatography. In two-dimensional chromatography, the effluent of one column, at a specific time or absorbance, can be directed onto a second column. This allows for a protein to be purified using two columns in a single chromatographic run.
Development of a Mathematical Model for Calculating the Cetane Number of Diesel Fuel Based on Their Hydrocarbon Composition and Intermolecular Interactions of Mixture Components
Published in Combustion Science and Technology, 2021
M.V. Maylin, E.V. Frantsina, A.A. Grinko
GC-MS (Gas Chromatograph with Mass Spectrometric Detector) system from Agilent. A mass spectrometric detector (in addition to the integrated FID) is a time-of-flight tube (QTOF), which allows to record ion masses up to 0.0001 amu, which significantly increases the resolution of the device compared to the standard GC-MS systems, where mass registration takes place generally with an accuracy of 0.1 amu. Moreover, the time-of-flight mass spectrometric detector allows to work in MS-MS mode, because of integrated hexapole collision cell. In MS-MS mode, it is possible to identify the most complex molecular structures. Also, this GC-MSQTOF is equipped with an LTM II module, which allows to work in two-dimensional chromatography mode (GCxGC). The GCxGC mode simplifies the work with complex matrices of organic substances, which are difficult or actually impossible to separate under the conditions of the standard one-dimensional mode (Lorentz et al. 2017, Soares et al. 2013). The full name of the device: Agilent 7890 (GC) – 7200 QTOF (MS) with the LTM-II module for two-dimensional chromatography.
Identification of hydrocarbon compositions of diesel fractions and assessment of their effect on fuel operational characteristics
Published in Petroleum Science and Technology, 2020
E. V. Frantsina, A. A. Grinko, N. I. Krivtsova, M. V. Maylin, A. A. Sycheva
The analysis of aromatic hydrocarbons was carried out in the mode of two-dimensional chromatography. The analyses of the qualitative and quantitative changes in the aromatic compounds in the straight-run and hydro-dewaxed diesel fractions showed that their total content decreased from 13.64 to 10.37% wt. This fact favors the improvement of the low-temperature properties and the starting characteristics of the fuel, which was proved by certain experimental data (Table 2). The aromatic compounds were represented by mono-, bi- and tri-aromatic hydrocarbons, where the content of monoaromatic (benzene derivatives) increased from 4.69 to 8.85% wt., whereas the content of biaromatic (naphthalene derivatives), on the contrary, decreased from 8.49 to 1.52% wt. At the same time the content of triaromatic hydrocarbons in the straight-run diesel fraction was insignificant and amounted to 0.47% wt. and in the hydro-dewaxed fraction they were completely absent. This fact about the change in the composition of the aromatic hydrocarbons is associated with the process in a hydrogen medium promoting hydrogenation of polycyclic aromatic compounds.
A review of extraction methods for the analysis of pharmaceuticals in environmental waters
Published in Critical Reviews in Environmental Science and Technology, 2020
Kevin D. Daniels, Minkyu Park, Zhenzhen Huang, Ai Jia, Guillermo S. Flores, Hian Kee Lee, Shane A. Snyder
Various approaches have been applied over the years to try and reduce the impact of matrix effects. A fundamental approach is to remove the matrix components responsible for the interference prior to MS analysis (Reemtsma, 2003). One way to remove the matrix compounds responsible for interference is to apply complexed SPE method, a two-step extraction to further clean up the sample during extraction, as shown in Figure 3. For example, Silica or MAX cartridges can be used after HLB cartridges to reduce the matrix effect when analyzing antibiotics (Hernando et al., 2004; Jia, Xiao, Hu, Asami, & Kunikane, 2009) and glucocorticoids (Jia, Wu, Daniels, & Snyder, 2016). For estrogens, florisil cartridges have been used after HLB cartridges to enhance the analysis of estrogens (Ingrand, Herry, Beausse, & De Roubin, 2003). Recently, molecularly imprinted polymers, which are highly specific, were applied as a cleanup step (Zorita et al., 2008). In addition to clean up steps with SPE, other matrix effects can be correlated to poor chromatographic separation (Kloepfer, Quintana, & Reemtsma, 2005). Ultra-high performance liquid chromatography can reduce some matrix effects that are observed during HPLC by narrowing elution bands (Wong & MacLeod, 2009). Two-dimensional chromatography, such as comprehensive two-dimensional gas chromatography (GC), has been applied where the sample underwent two chromatographic separations (Pascoe, Foley, & Gusev, 2001), resulting in detection limits comparable to HPLC-MS/MS (Matamoros, Jover, & Bayona, 2010). Diluting the sample can reduce matrix effects; however, it would also increase detection limits (Hernando et al., 2004).