Improved Protein Hydrogen/Deuterium Exchange Mass Spectrometry Platform with Fully Automated Data Processing

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine

Improved Protein Hydrogen/Deuterium Exchange Mass Spectrometry Platform with Fully Automated Data Processing

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine

Time-Resolved Energy-Momentum Spectroscopy of Electric and Magnetic Dipole Transitions in Cr³⁺:MgO

Due to the recent interest in magnetic light-matter interactions, the magnetic dipole (MD) transitions in lanthanide ions have been studied for potential applications in nano-optics. Similar to lanthanide ions, transition-metal ions also exhibit strong MD emission at room temperature, but their prominent MD zero-phonon lines are often accompanied by significant electric dipole (ED) sideband emission. Here, we extend energy-momentum spectroscopy to time-resolved measurements, and use this technique to quantify the ED and MD contributions to light emission from trivalent chromium doped magnesium oxide (Cr³⁺:MgO). This allows us to differentiate the MD ²E → ⁴A₂ zero-phonon line from phonon-assisted ²E → ⁴A₂ and ⁴T₂ → ⁴A₂ ED sidebands. We also demonstrate how the relative intensities of the sharp MD zero-phonon line and the broad ED sidebands can be used as a qualitative measure of the MD and ED local density of optical states

sj-xlsx-7-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-xlsx-7-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-jpg-9-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-jpg-9-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-xlsx-3-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-xlsx-3-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-xlsx-5-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-xlsx-5-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-docx-1-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-docx-1-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-xlsx-4-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-xlsx-4-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p

sj-xlsx-2-onc-10.1177_11795549231199915 – Supplemental material for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas

Supplemental material, sj-xlsx-2-onc-10.1177_11795549231199915 for SPAG5 Expression Predicts Poor Prognosis and is Associated With Adverse Immune Infiltration in Lung Adenocarcinomas by Gang Xiao, Xie Xu, Zhibo Chen, Jie Zeng and Jianjiang Xie in Clinical Medicine Insights: Oncology</p