Dynamx software

Manufactured by Waters Corporation

Sourced in United States

DynamX software is a data analysis tool developed by Waters Corporation. It is designed to process and analyze data generated from various analytical instruments. The software provides tools for visualizing, processing, and interpreting data, enabling users to gain insights from their experimental results.

Automatically generated - may contain errors

Lab products found in correlation

Proteinlynx global server, by Waters Corporation (3 mentions) Proteinlynx global server software, by Waters Corporation (2 mentions) Proteinlynx software, by Waters Corporation (1 mentions) Immobilized pepsin column, by Waters Corporation (1 mentions) Nano lc system, by Waters Corporation (1 mentions) C18 analytical column, by Waters Corporation (1 mentions) Plgs software, by Waters Corporation (1 mentions) Poroszyme immobilized pepsin cartridge, by Thermo Fisher Scientific (1 mentions) Synapt g1 mass spectrometer, by Waters Corporation (1 mentions)

8 protocols using dynamx software

HDX-MS Analysis of mAb7 and PLBL2 Interaction

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Example 7

In order to have a further understanding of the science underlying interactions of mAb7 and PLBL2, HDX-MS analysis of mAb7 and mAb7 bound with PLBL2 samples were performed using a Waters HDX manager system coupled to a Synapt G2-S mass spectrometer. Based on the K_Dof 40.0 μM by SPR, ˜70% of mAb is bound with PLBL2 after deuterium labelling. Deuterium labelling was measured at 0.5 min, 5 min, 60 min, 120 min, 180 min, and 240 min. The data were analyzed using Waters DynamX software and generated HDX differential plot (FIG. 7). Vertical sticks represent the total HDX differences of each peptide from six labelling time points. Comparison of the HDX profile of unbound and PLBL2-bound mAb7 reveals that region K218-F256 in heavy chain show a reduction in deuterium uptake upon binding to PLBL2. This indicates a stabilization of this region due to PLBL2 binding to mAb7 and correlates well with other experimental binding results.

US11254753B2. Antibodies with reduced binding to process impurities (2022-02-22). GlaxoSmithKline Intellectual Property Development Limited [GB]. Inventors: Hella Bosteels [GB], Shugui Chen [US], Kayeleigh Farrow [GB], Richard Kucia-Tran [GB], William John Kenneth Lewis [GB], Andrew S. Thomson [US], Mark Uden [GB].

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Hydrogen-Deuterium Exchange Mass Spectrometry

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Sample protein was exposed to 100% D₂O buffer for various incubation times and the reaction quenched by trifluoroacetic acid prior to mass spectrometry. In order to increase the resolution in terms of amino acid sequence, the quenched sample was subjected to pepsin digestion. Prior to ESI mass spectrometry, the peptides were seperated on an HPLC column to further increase resolution. The whole process was carried out in Waters nanoACQUITY UPLC Hydrogen Deuterium Exchange (HDS) System (Waters Corporation; Milford, MA). Data were recorded and analyzed by ProteinLynx software (ProteinLynx Global Server, Waters Corporation). The peptide spectra assignment for each identified peptide in the undeuterated sample as well as in the subsequent deuterated samples was carried out using the DynamX software (Waters Corporation). The output file was converted to a Microsoft Excel format (Microsoft, Redmond, WA) for further data analysis. The back-exchange constant used for calculating the exchange rate was 1.49.

Hu W., Anand G., Sivaraman J., Leung K.Y, & Mok Y.K. (2014). A Disordered Region in the EvpP Protein from the Type VI Secretion System of Edwardsiella tarda is Essential for EvpC Binding. PLoS ONE, 9(11), e110810.

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Peptide Deuterium Uptake Analysis

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Non-deuterated digested peptides were identified by mass accuracy and MS/MS fragmentation (Waters HDMSe function) using the ProteinLynx Global Server software (Waters Corp., MA, USA). Fragmentation (HDMSe) of non-deuterated peptides was activated in the transfer cell with the collision energy ramp from 15 to 65 V. The level of deuterium calculation on individual peptides was determined using the DynamX software (Waters Corp., MA, USA). HDX data were analyzed by calculating and summing the difference in deuterium uptake for identical peptides between the two states, PTx and gdPT, at all the HDX mixing time points. The data are all shown with respect to gdPT. Hence, positive or negative values indicate an increase or decrease in deuterium uptake in gdPT, whereas neutral value indicates no difference of the peptides. A difference of 1.5 Da and 3σ (3× standard deviation of a given peptide over the five time course) was set as the statistically significant threshold. A summary of HDX data corresponding to all peptides in the study is provided in Supplementary Data 1.

Ausar S.F., Zhu S., Duprez J., Cohen M., Bertrand T., Steier V., Wilson D.J., Li S., Sheung A., Brookes R.H., Pedyczak A., Rak A, & Andrew James D. (2020). Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Communications Biology, 3, 427.

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Structural Comparison of Ranibizumab Variants

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Hydrogen/deuterium exchange-mass spectrometry (H/DX-MS) was adapted to compare higher order structures between ranibizumab samples. H/DX-MS was initiated by a 1:8 dilution of sample in D₂O buffer at intervals of 10 s, 1 min, 10 min, 1 h, and 4 h before quenching and injecting into the mass spectrometer. Peptides were digested on an immobilized pepsin column, and the trapped peptide fragments were eluted by a gradient of 8% to 92% acetonitrile in 15 min. Mass spectra were collected in MS^E mode, and data were analyzed by ProteinLynX Global Server™ (Waters) to identify peptides and by DynamX software (Waters) to calculate deuterium uptake and generate butterfly and difference plots.

Kim E., Han J., Chae Y., Park H., Kim S., Kim S., Lee J, & Kim B.C. (2022). Evaluation of the Structural, Physicochemical, and Biological Characteristics of SB11, as Lucentis® (Ranibizumab) Biosimilar. Ophthalmology and Therapy, 11(2), 639-652.

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Eculizumab Hydrogen/Deuterium Exchange

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Hydrogen/deuterium exchange-MS (H/DX-MS) was initiated by dilution of eculizumab (SB12 and RP) in D₂O buffer for 10 s, 1 min, 10 min, 1 h and 4 h. After labeling, the solution was mixed with quenching buffer and injected into the Waters nano LC system. Loaded protein was digested on an immobilized pepsin column (Waters) and the digested peptide fragments was separated on an analytical C18 column (Waters). The analyte was then introduced to MS with MS^E mode. Mass spectra were analyzed using PLGS software (Waters) for peptide identification, and DynamX software (Waters) for deuterium uptake calculation and generation of the butterfly plot and uptake plots.

Kim H., Hong E., Lee J., Hong S., Kim J., Cho M., Kim Y, & Yoo T. (2023). Characterization for the Similarity Assessment between Proposed Biosimilar SB12 and Eculizumab Reference Product Using a State-of-the-Art Analytical Method. Biodrugs, 37(4), 569-581.

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Mapping Ligand-Dependent Dynamics of C-GRIFIN

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Identified peptic peptides obtained by the digestion of C-GRIFIN were organized as list using the Protein Lynx Global Server software (Waters) and the MSE data for the undeuterated controls. By applying DynamX software (Waters), the relative deuterium uptake for each identified peptide was calculated by subtracting the centroid masses of the corresponding peptides found in the undeuterated and deuterated samples, for both ligand-loaded and ligand-free C-GRIFIN. The ligand-dependent difference in relative deuterium uptake was determined using DynamX, and its significance was evaluated by calculating a two-sided confidence limit with a significance level of 0.02 [32 (link)]. The result of this evaluation was visualized by color coding of β-strands in the three-dimensional model of C-GRIFIN.

Ruiz F.M., Gilles U., Ludwig A.K., Sehad C., Shiao T.C., García Caballero G., Kaltner H., Lindner I., Roy R., Reusch D., Romero A, & Gabius H.J. (2017). Chicken GRIFIN: Structural characterization in crystals and in solution. Biochimie, 146, 127-138.

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HDX-MS Analysis of Protein Dynamics and Epitope Mapping

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ProteinLynx Global Server (Waters Corp., MA, USA) was used for peptide identification and DynamX software (Waters Corp., MA, USA) was used for analysis of deuterium exchange on identified peptides. Only peptides with high product per amino acid score and spectral quality were considered. The summed difference over all timepoints were used for comparison evaluations.
Back-Exchange correction factor was not applied in this study as comparison of same peptides were made for different protein states. However, based on the previous publication and study^{45 (link)}, the back-exchange was calculated to be on average of 29.9% using 11 enolase peptides. In adherence to the recommended guideline for HDX-MS experiment reporting, the raw HDX-MS data for both states are attached in the supplementary information^{46 (link)}.
For dynamic analysis, the deuterium differences were then mapped onto representative Beta structures (PDB: 7LYQ). For epitope mapping of mAb 511, the deuterium differences were mapped on representative ancestral structure (PDB: 6VSB).

Bruch E.M., Zhu S., Szymkowicz L., Blake T., Kiss T., James D.A., Rak A., Narayan K., Balmer M.T, & Chicz R.M. (2024). Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Scientific Reports, 14, 2038.

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Deuterium Pulse-labeling Protein Refolding

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Refolding reactions were essentially performed as above. Aliquots were withdrawn at different times and pulse-labeled for 12 s by 10-fold dilution with buffer E (20 mM Tris-HCl, 20 mM KCl, pD 7.5, 99.9% D₂O) to a final concentration of 90 % D₂O, followed by acid quenching (Figure 4A). Intact proteins were immediately analyzed by LC-MS on a Waters Synapt G1 mass spectrometer. To obtain H/DX data at peptide resolution, acid quenched samples were injected into an H/DX Waters nanoACQUITY UPLC (Wales et al., 2008 (link)) and passed through a Poroszyme immobilized pepsin cartridge (Applied Biosystems). Peptic peptides eluting from the pepsin column were trapped, desalted and then separated in 6 min with a 8-40 % acetonitrile gradient in 0.1 % formic acid pH 2.5. All chromatographic elements were held at 2.5°C. The average amount of back-exchange was 20-25 % (Wales et al., 2008 (link)). All experiments were performed between 2-4 times. Mass spectra were processed with DynamX software (Waters Corp., Milford, MA, USA). See Extended Experimental Procedures for detailed description.

Georgescauld F., Popova K., Gupta A.J., Bracher A., Engen J.R., Hayer-Hartl M, & Hartl F.U. (2014). GroEL/ES Chaperonin Modulates the Mechanism and Accelerates the Rate of TIM-Barrel Domain Folding. Cell, 157(4), 922-934.

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