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Zihao Qi, Wysocki Lab, Ohio State, “Native Mass Spectrometry of Single Strand Annealing Protein and Nucleoprotein Complexes” and Enoch Amoah, Badu Lab, Ohio State, “Mass Spectrometry Approach for Differentiation of Positional Isomers of Saccharides: Toward Direct Analysis of Rare Sugars” Date: February 21, 2022 Time: 5:30 PM Eastern Location: DHLRI 170

AlphaFold2 has revolutionized protein structure prediction from amino-acid sequence. In addition to protein structures, high-resolution dynamics information about various protein regions is important for understanding protein function. Although AlphaFold2 has neither been designed nor trained to predict protein dynamics, it is shown here how the information returned by AlphaFold2 can be used to predict dynamic protein regions at the individual residue level. The approach, which is termed cdsAF2,...

AlphaFold2 has revolutionized protein structure prediction from amino-acid sequence. In addition to protein structures, high-resolution dynamics information about various protein regions is important for understanding protein function. Although AlphaFold2 has neither been designed nor trained to predict protein dynamics, it is shown here how the information returned by AlphaFold2 can be used to predict dynamic protein regions at the individual residue level. The approach, which is termed cdsAF2,...

We are canceling this month’s MSDG meeting. Instead, we encourage people to please attend seminars by analytical faculty candidates. Originally scheduled speakers for January will present at February’s meeting. Meeting schedule.

Emily Sekera, Hummon Lab, Ohio State. “Mass Spectrometry Imaging of 3D Cell Cultures: From Drug Treatments to Dietary Changes” Date: December 13, 2022 Time: 5:30 PM Location: BRT 115

Dr. Andrew Arslanian, Wysocki Group, Ohio State. “Gas Phase Techniques for the Study of Biomolecular and Supramolecular Structures and Chemistry” Date: November 15, 2022 Time: 5:30 PM Eastern Location: CBEC 267

Total joint arthroplasty is a common surgical procedure resulting in improved quality of life; however, a leading cause of surgery failure is infection. Periprosthetic joint infections often involve biofilms, making treatment challenging. The metabolic state of pathogens in the joint space and mechanism of their tolerance to antibiotics and host defenses are not well understood. Thus, there is a critical need for increased understanding of the physiological state of pathogens in the joint space...

Total joint arthroplasty is a common surgical procedure resulting in improved quality of life; however, a leading cause of surgery failure is infection. Periprosthetic joint infections often involve biofilms, making treatment challenging. The metabolic state of pathogens in the joint space and mechanism of their tolerance to antibiotics and host defenses are not well understood. Thus, there is a critical need for increased understanding of the physiological state of pathogens in the joint space...

Prof. David Russell, Texas A&M University, “Advanced MS Technologies for Studies for Biomolecule Complexes: Structure, Stability and Dynamics” Date: October 3, 2022 Time: 5:30 PM EST Location: CBEC 130

Mr. Alex Grooms, Badu Lab, Ohio State, “Plasma-Droplet Reaction Systems: A Direct Mass Spectrometry Approach for Enhanced Characterization of Lipids at Multiple Isomer Levels” Date: September 20, 2022 Time: 5:30 PM EST Location: CBEC 267

An NMR supersequence is introduced for the rapid acquisition of ^(15)N-CEST and methyl-^(13)C-CEST experiments in the same pulse sequence for applications to proteins. The high sensitivity and accuracy allows the simultaneous quantitative characterization of backbone and side-chain dynamics on the millisecond timescale ideal for routine screening for alternative protein states.

An NMR supersequence is introduced for the rapid acquisition of ^(15)N-CEST and methyl-^(13)C-CEST experiments in the same pulse sequence for applications to proteins. The high sensitivity and accuracy allows the simultaneous quantitative characterization of backbone and side-chain dynamics on the millisecond timescale ideal for routine screening for alternative protein states.

Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D ^(13)C-¹H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the...

Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D ^(13)C-¹H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the...

Prof. Anyin Li, University of New Hampshire Date: April 19th, 2022 Time: 5:30 PM EST Zoom: https://osu.zoom.us/j/96434729214?pwd=R0U1K3hyZ2M1a1ZYR296eVRLcTVlZz09 Meeting ID: 964 3472 9214 Password: 859213

Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and...

Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and...

1. Mr. Taghi Sahraeian, Badu Research Group “Air-Tight Ambient Mass Spectrometry for Direct Analysis of Solid-Electrolyte Interphase of Li-Ion Battery” 2. Second student volunteer speaker is needed Date: March 29th, 2022 Time: 5:30 PM EST Zoom: https://osu.zoom.us/j/96434729214?pwd=R0U1K3hyZ2M1a1ZYR296eVRLcTVlZz09 Meeting ID: 964 3472 9214 Password: 859213

There is a critical need to accurately diagnose, prevent, and treat biofilms in humans. The biofilm forming P. aeruginosa bacteria can cause acute and chronic infections, which are difficult to treat due to their ability to evade host defenses along with an inherent antibiotic-tolerance. Using an untargeted NMR-based metabolomics approach, we identified statistically significant differences in 52 metabolites between P. aeruginosa grown in the planktonic and lawn biofilm states. Among them, the...

There is a critical need to accurately diagnose, prevent, and treat biofilms in humans. The biofilm forming P. aeruginosa bacteria can cause acute and chronic infections, which are difficult to treat due to their ability to evade host defenses along with an inherent antibiotic-tolerance. Using an untargeted NMR-based metabolomics approach, we identified statistically significant differences in 52 metabolites between P. aeruginosa grown in the planktonic and lawn biofilm states. Among them, the...