A5030033275- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Epigenetics and DNA Methylation
- Ubiquitin and proteasome pathways
- Microbial Natural Products and Biosynthesis
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Protein Degradation and Inhibitors
- Cancer-related gene regulation
- RNA and protein synthesis mechanisms
- Ion-surface interactions and analysis
- Glioma Diagnosis and Treatment
- Ferroptosis and cancer prognosis
- Cancer-related molecular mechanisms research
- Analytical Chemistry and Chromatography
- Fungal Biology and Applications
- Analytical chemistry methods development
- Plant biochemistry and biosynthesis
- Histone Deacetylase Inhibitors Research
- Biochemical and Molecular Research
- Malaria Research and Control
- Monoclonal and Polyclonal Antibodies Research
- Biomedical Text Mining and Ontologies
Radiometrics (United States)
2024
Lumetrics (United States)
2024
Northwestern University
2013-2022
Digital Proteomics (United States)
2013-2021
Defence Science and Technology Laboratory
2018
Robert H. Lurie Comprehensive Cancer Center of Northwestern University
2013-2017
University of Illinois Urbana-Champaign
2006-2011
Scripps Institution of Oceanography
2009
Johns Hopkins University
2008
Urbana University
2008
The top-down approach to proteomics offers compelling advantages due the potential provide complete characterization of protein sequence and post-translational modifications. Here we describe implementation 193 nm ultraviolet photodissociation (UVPD) in an Orbitrap mass spectrometer for intact proteins. Near-complete fragmentation proteins up 29 kDa is achieved with UVPD including unambiguous localization a single residue mutation several modifications on Pin1 (Q13526), implicated...
The human appendix is a reservoir for α-synuclein aggregates and its removal may reduce the risk of Parkinson’s disease.
Many top-down proteomics experiments focus on identifying and localizing PTMs other potential sources of “mass shift” a known protein sequence. A simple application to match ion masses facilitate the iterative hypothesis testing PTM presence location would assist with data analysis in these experiments. ProSight Lite is free software tool for matching single candidate sequence against set mass spectrometric observations. Fixed or variable modifications, including both select number...
Abstract Cell-free protein synthesis has emerged as a powerful approach for expanding the range of genetically encoded chemistry into proteins. Unfortunately, efforts to site-specifically incorporate multiple non-canonical amino acids proteins using crude extract-based cell-free systems have been limited by release factor 1 competition. Here we address this limitation establishing bacterial platform based on genomically recoded Escherichia coli lacking 1. This was developed exploiting...
Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma blood bone marrow. The results, compiled Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level are specific indicators...
Lantibiotics are ribosomally synthesized peptides that undergo posttranslational modifications to their mature, antimicrobial form. They characterized by the unique amino acids lanthionine and methyllanthionine, introduced means of dehydration Ser/Thr residues followed reaction resulting dehydro with cysteines form thioether linkages. Two-component lantibiotics use two each posttranslationally modified yield functionally distinct products act in synergy provide bactericidal activity. By...
Top-down proteomics has improved over the past decade despite significant challenges presented by analysis of large protein ions. Here, detection these high mass species electrospray-based spectrometry (MS) is examined from a theoretical perspective to understand mass-dependent increases in number charge states, isotopic peaks, and interfering present typical spectra. Integrating effects into quantitative model captures reduced ability detect 25 kDa with speed sensitivity characteristic...
PksA, which initiates biosynthesis of the environmental carcinogen aflatoxin B1, is one multidomain iterative polyketide synthases (IPKSs), a large, poorly understood family biosynthetic enzymes. We found that dissection PksA and its reconstitution from selected sets domains allows accumulation characterization advanced octaketide intermediates bound to enzyme, permitting reactions controlled by individual catalytic be identified. A product template (PT) domain unites with ketosynthase...
Pharmaceuticals are a class of emerging contaminants whose fate in the wastewater treatment process has received increasing attention past years. Acidic pharmaceuticals (ibuprofen, naproxen, mefenamic acid, ketoprofen, and diclofenac), caffeine, antibacterial triclosan were quantified at four different steps from three urban plants. The compounds extracted samples on Waters Oasis hydrophilic-lipophilic balance solid-phase extraction columns, silylated, analyzed by gas chromatography-mass...
The primary structural information of proteins employed as biotherapeutics is essential if one wishes to understand their structure-function relationship, well in the rational design new therapeutics and for quality control. Given both large size (around 150 kDa) complexity intact immunoglobulin G (IgG), which includes a variable number disulfide bridges, its extensive fragmentation subsequent sequence determination by means tandem mass spectrometry (MS) are challenging. Here, we applied...
Amyloid-beta (Aβ) plays a key role in the pathogenesis of Alzheimer's disease (AD), but little is known about proteoforms present AD brain. We used high-resolution mass spectrometry to analyze intact Aβ from soluble aggregates and insoluble material brains six cases with severe dementia pathologically confirmed AD. The are especially relevant because they believed be most toxic form Aβ. found diversity peptides, 26 unique including various N- C-terminal truncations. truncations comprised 73%...
Top-down proteomics is emerging as a viable method for the routine identification of hundreds to thousands proteins. In this work we report largest top-down study date, with 1,220 proteins from transformed human cell line H1299 at false discovery rate 1%. Multiple separation strategies were utilized, including focused isolation mitochondria, resulting in significantly improved proteome coverage relative previous work. all, 347 mitochondrial identified, ~50% below 30 kDa and over 75% subunits...
We have developed a targeted method to quantify all combinations of methylation on an H3 peptide containing lysines 27 and 36 (H3K27-K36). By using stable isotopes that separately label the histone backbone its methylations, we tracked rates demethylation in myeloma cells expressing high vs. low levels methyltransferase MMSET/WHSC1/NSD2. Following quantification 99 labeled H3K27-K36 states across time, kinetic model converged yield 44 effective rate constants qualifying each step as function...
Using iron to generate a copper ligand Many microbial enzymes are metal-dependent, and the microbe must acquire scarce metals from environment. Microbes that use methane as carbon source have copper-dependent enzyme oxidizes methane. Peptides known methanobactins (Mbns) by using pair of ligands comprising nitrogen-containing ring an adjacent thioamide. Kenney et al. describe biosynthetic machinery adds copper-binding groups precursor peptide. This involves complex two homologs: MbnB, member...
With the prospect of resolving whole protein molecules into their myriad proteoforms on a proteomic scale, question quantitative analysis in discovery mode comes to fore. Here, we demonstrate robust pipeline for identification and stringent scoring abundance changes forms <30 kDa complex system. The input is ∼100–400 μg total each biological replicate, outputs are graphical displays depicting statistical confidence metrics proteoform (i.e., volcano plot representations technical variation)....