A5029387280- Geophysics and Gravity Measurements
- Ionosphere and magnetosphere dynamics
- Methane Hydrates and Related Phenomena
- Solar and Space Plasma Dynamics
- Seismic Waves and Analysis
- Astrophysics and Cosmic Phenomena
- Earthquake Detection and Analysis
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Seismology and Earthquake Studies
- Metabolomics and Mass Spectrometry Studies
- Ion-surface interactions and analysis
- Analytical Chemistry and Chromatography
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Peptidase Inhibition and Analysis
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Analytical chemistry methods development
- Ubiquitin and proteasome pathways
- Biochemical and biochemical processes
- Health, Environment, Cognitive Aging
- SARS-CoV-2 and COVID-19 Research
Environmental Molecular Sciences Laboratory
2016-2025
Pacific Northwest National Laboratory
2016-2025
Zhejiang University
2023-2025
National Energy Technology Laboratory
2023
Battelle
2021-2023
Richland College
2015-2020
The Ohio State University
2013-2019
Center for Drug Evaluation and Research
2015
United States Food and Drug Administration
2015
University of Arizona
2012-2013
The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by human genome. However, proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors translation, post-translational modifications result a depth estimated at several million unique proteoforms. Recently mass spectrometry been demonstrated landmark efforts mapping proteoform landscape bulk analyses. Herein, we developed an...
The quaternary structures of proteins are both important and interest to chemists, because many exist as complexes in vivo, probing these allows us better understand their biological functions. Conventional structural biology methods such X-ray crystallography nuclear magnetic resonance provide high-resolution information on the protein gold standards field. However, other emerging biophysical that only low-resolution data (e.g. stoichiometry subunit connectivity) also becoming more...
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess current state of top-down mass spectrometry (TD MS) and middle-down (MD characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet needs rapidly growing therapeutic market, it is important develop analytical strategies characterize heterogeneity a product's structure accurately reproducibly. major objective determine whether TD/MD MS technologies...
Significance There is a large gap between the number of protein complex structures currently solved and functionally relevant structures. Mass spectrometry-based approaches for biomacromolecule structural characterization are growing, beginning to fill critical gaps, complement other biology tools. We have shown several examples that collision ions with surface yields products reflective substructure. present here computational model predicts relative appearance energy at which globular...
The intracellular pathogen Legionella pneumophila delivers more than 330 effectors into host cells by its Dot/Icm secretion system. Those direct the biogenesis of -containing vacuole (LCV) that permits survival and replication. It has long been documented LCV is associated with mitochondria a number have shown to target this organelle. Yet, biochemical function cell most these remain unknown. Here, we found substrate Ceg3 (Lpg0080) mono-ADP-ribosyltransferase localizes in where it attacks...
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits improvements in fractionation, separation, fragmentation, and analysis. The algorithms to match MS/MS sequences have undergone a parallel evolution, with both spectral alignment match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art for identification (ProSight PD, TopPIC, MSPathFinderT, pTop) their yield PrSMs while controlling...
Tandem mass spectrometry is a tool to dissect noncovalent protein complexes into smaller substructures for quaternary structure analysis. The commonly used activation method, collision induced dissociation (CID), often provides limited structural information from the typical pattern where unfolded monomers are ejected complex. In contrast, surface-induced (SID) has been shown be very effective at dissociating with less unfolding than CID. We present here SID of large tetradecamer protein,...
Crash survival: Several noncovalent protein complexes were dissociated by surface collision and studied using ion mobility mass spectrometry. Most of the resulting monomer products some undissociated precursors maintain overall size shape their native fold after impact. This result is in contrast to unfolding structures observed for commonly used activation involving neutral gas collisions.
Charge states of noncovalent protein complexes in the gas phase are known to affect their propensity for unfolding and dissociation. In this work, C-reactive (CRP) pentamer Concanavalin A (ConA) tetramer at different charge were subjected collision induced dissociation (CID) surface (SID) a modified quadrupole/ion mobility/time-of-flight mass spectrometer. manipulation was achieved through solution addition reducing (triethylammonium acetate) or supercharging (3-nitrobenzylalcohol) reagents....
Abstract Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist structural characterization the enzymes responsible biomineralization. The active oxidase in Bacillus sp. PL-12, Mnx, is a complex composed multicopper (MCO), MnxG, and...
A custom in-line surface-induced dissociation (SID) device has been incorporated into a commercial ion mobility quadrupole/time-of-flight mass spectrometer in order to provide an alternative and potentially more informative activation method than the commonly used collision-induced (CID). Complicated sample mixtures can be fractionated by (IM) then dissociated CID or SID for further structural analysis. Interpretation of spectra cesium iodide clusters was greatly simplified with IM prior...
One attractive feature of ion mobility mass spectrometry (IM-MS) lies in its ability to provide experimental collision cross section (CCS) measurements, which can be used distinguish different conformations that a protein complex may adopt during gas-phase unfolding. However, CCS values alone give no detailed information on subunit structure within the complex. Consequently, structural characterization typically requires molecular modeling, have uncertainties without support. method...
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down the inability to analyze low amount biological samples, which limits its access isolated rare cells, fine needle aspiration biopsies, tissue substructures. Herein, we developed an ultrasensitive platform by incorporating microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in...
Proteomic investigations of Alzheimer's and Parkinson's disease have provided valuable insights into neurodegenerative disorders. Thus far, these largely been restricted to bottom-up approaches, hindering the degree which one can characterize a protein's "intact" state. Top-down proteomics (TDP) overcomes this limitation; however, it is typically limited observing only most abundant proteoforms relatively small size. Therefore, fractionation techniques are commonly used reduce sample...
SARS-CoV-2 has caused a global pandemic, and taken over 1.7 million lives as of mid-December, 2020. Although great progress been made in the development effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines market, there is still an unmet need essential antiviral drugs therapeutic impact for treatment moderate-to-severe COVID-19. Towards this goal, high-throughput assay was used screen nsp15 uracil-dependent endonuclease (endoU) function...
Conventional proteomic approaches measure the averaged signal from mixed cell populations or bulk tissues, leading to dilution of signals arising subpopulations cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping cellular heterogeneity tissue microenvironments. However, cannot unambiguously define and quantify proteoforms, which are intact (i.e., functional) forms proteins capturing genetic variations, alternatively spliced...
Top-down proteomics is an emerging analytical strategy to characterize combinatorial protein post-translational modifications (PTMs). However, sample complexity and small mass differences between chemically closely related proteoforms often limit the resolution attainable by separations employing a single liquid chromatographic (LC) principle. In particular, for ultramodified proteins like histones, extensive time-consuming fractionation needed achieve deep proteoform coverage. Herein, we...
The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background can cause structural changes ranging from unfolding subunit dissociation. Additionally, recent studies have highlighted role of charge such changes, but mechanism not completely understood. In this study, top down (native TD) mass spectrometry was used probe gas-phase alcohol dehydrogenase (ADH, 4mer) under varying...
Core histones including H2A, H2B, H3, and H4 are key modulators of cellular repair, transcription, replication within eukaryotic cells, playing vital roles in the pathogenesis disease responses to environmental stimuli. Traditional mass spectrometry (MS)-based bottom-up top-down proteomics allows for comprehensive identification proteins post-translational modification (PTM) harboring proteoforms. However, these methodologies have difficulties preserving near-cellular spatial distributions...
SARS-CoV-2 cellular infection is mediated by the heavily glycosylated spike protein. Recombinant versions of protein and receptor-binding domain (RBD) are necessary for seropositivity assays can potentially serve as vaccines against viral infection. RBD plays key roles in protein's structure function, thus, comprehensive characterization recombinant critically important biopharmaceutical applications. Liquid chromatography coupled to mass spectrometry has been widely used characterize...