A5006295902- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Electrochemical sensors and biosensors
- Analytical Chemistry and Sensors
- Glycosylation and Glycoproteins Research
- Molecular Junctions and Nanostructures
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Microfluidic and Capillary Electrophoresis Applications
- Monoclonal and Polyclonal Antibodies Research
- Pancreatic function and diabetes
- Dendrimers and Hyperbranched Polymers
- Ubiquitin and proteasome pathways
- Gene expression and cancer classification
- RNA modifications and cancer
- Advanced Fluorescence Microscopy Techniques
- Enzyme Structure and Function
University of Wisconsin–Madison
2015-2025
Madison Group (United States)
2018-2025
Division of Chemistry
2013
University of California, Irvine
2008
Saint Michael's College
2007
Medical College of Wisconsin
2005
Third Wave Systems (United States)
2002-2004
Northwestern University
2002
Iowa State University
2000-2001
Ames National Laboratory
2000-2001
A new optical sensor based on covalent immobilization of a newly synthesized calcium-selective, long-wavelength, fluorescent indicator has been constructed, with response dynamic range optimal for physiological measurements. Immobilization occurs via photoinitiated copolymerization the acrylamide distal end silanized 125 μm diameter multimode fiber. The working lifetime this is limited only by photobleaching indicator. Due to inherent hydrophilic nature polymer, time governed simple aqueous...
Correct identification of protein post-translational modifications (PTMs) is crucial to understanding many aspects function in biological processes. G-PTM-D a recently developed technique for global and localization PTMs. Spectral file calibration prior applying G-PTM-D, algorithmic enhancements the peptide database search significantly increase accuracy, speed, scope PTM identification. We enhance by using multinotch searches demonstrate its effectiveness numerous types PTMs including...
We have studied the dynamics of directed, multistep energy transport in a class fractal-like dendrimeric molecules. For particular forms these highly branched phenylacetylene dendrimers, both theory and experiment put lowest excitation at center (locus) supermolecule. This results structurally symmetric ordered exciton funnel, with well-directed gradient. designed synthesized derivative dendrimers perylene moiety locus, which acts as an trap for directed funnel. Spectroscopic evidence...
Direct experimental evidence is presented for the existence of localized excitations on fractal supermolecular structures that may serve as photonic antenna systems. For one dendrimer family electronic spectra show no redshift with system size, indicating are at nodes Cayley trees describing these ordered structures. In contrast, similar dendrimers varying lengths molecular branches exhibit a decrease in band edge energy growing size system, consistent hierarchy localization lengths. The...
Human proteomic databases required for MS peptide identification are frequently updated and carefully curated, yet still incomplete because it has been challenging to acquire every protein sequence from the diverse assemblage of proteoforms expressed in tissue cell type. In particular, alternative splicing shown be a major source this cell-specific variation. Many new splice forms have detected at transcript level using next generation sequencing methods, especially RNA-Seq, but is not known...
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...
The rapid and accurate quantification of peptides is a critical element modern proteomics that has become increasingly challenging as proteomic data sets grow in size complexity. We present here FlashLFQ, computer program for high-speed label-free following search bottom-up mass spectrometry data. FlashLFQ approximately an order magnitude faster than established methods. increased speed makes it practical to base upon all the charge states given peptide rather solely state was selected MS2...
The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics preeminent method for detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match sample; neither a subset nor superset database ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used predict isoforms.
An extension into the fluorescence mode of ion-exchange optodes is described, allowing miniaturization and its concomitant benefits. A micrometer-size, fluorescent fiber-optic sodium sensor based on a highly sodium-selective, crown ether-capped calix[4]arene ionophore, capable ratiometric operation. Three configurations are given, employing different lipophilic, pH chromoionophores (Nile Blue derivatives), demonstrating ability to improve detection limit tune dynamic range desired region...
Each individual carries thousands of nonsynonymous single nucleotide variants (nsSNVs) in their genome, each corresponding to a amino acid polymorphism (SAP) the encoded proteins. It is important be able directly detect and quantify these variations at protein level study post-transcriptional regulation, differential allelic expression, other biological processes. However, such variant peptides are not generally detected standard proteomic analyses due absence from generic databases that...
Current practice in mass spectrometry (MS)-based proteomics is to identify peptides by comparison of experimental spectra with theoretical derived from a reference protein database; however, this strategy necessarily fails detect peptide and sequences that are absent the database. We others have recently shown customized proteomic databases RNA-Seq data can be employed for MS-searching both improve MS analysis novel peptides. While general constitutes significant advance discovery...
A new global post-translational modification (PTM) discovery strategy, G-PTM-D, is described. proteomics database containing UniProt-curated PTM information supplemented with potential types and sites discovered from a first-round search of mass spectrometry data ultrawide precursor tolerance. second-round employing the conducted standard narrow tolerances yields deep coverage rich variety peptide modifications high confidence in complex unenriched samples. The G-PTM-D strategy represents...
The conformational dynamics and adsorption/desorption behavior of individual λ-DNA molecules at liquid−solid interfaces were monitored by imaging within the evanescent field layer using total internal reflection fluorescence microscopy. At a fused-silica surface, molecular conformation adsorption found to depend on both pH buffer composition. A histogram durations measured hydrodynamically flowing along interface exhibited asymmetry nearly identical that corresponding elution peaks in...
Most patients at risk for developing type 2 diabetes are hyperinsulinemic. Hyperinsulinemia may be a response to insulin resistance, but another possible abnormality is hypersecretion. BTBR mice resistant and When the leptin(ob) mutation introgressed into mice, they develop severe diabetes. We compared responsiveness of lean B6 mouse islets various secretagogues. The transamination product leucine, alpha-ketoisocaproate (KIC), elicited dramatic secretory in islets. KIC was blocked by...
Cell surface carbohydrates play important roles in a wide variety of biological processes including cell adhesion, fertilization, differentiation, development, and tumor metastasis. Lectins are proteins nonimmune origin which recognize bind to specific carbohydrate structural epitopes. We have recently described the development use lectin arrays as tools for elucidation structures expressed on surfaces. In present work this technology is employed characterization differences expression...
Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety cross-linkers are well developed, but reliable, rapid, user-friendly tools large-scale cross-linked proteins still in need. Here we report MetaMorpheusXL, a new search module within MetaMorpheus software suite that identifies both MS-cleavable noncleavable peptides MS data. MetaMorpheusXL ion-indexing algorithm,...
Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify post-translational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to searching enables global PTM (G-PTM) by exclusively looking curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified over 2200 unique, high-confidence modified peptides comprising 26 different...
Proteomics is presently dominated by the "bottom-up" strategy, in which proteins are enzymatically digested into peptides for mass spectrometric identification. Although this approach highly effective at identifying large numbers of present complex samples, digestion renders it impossible to identify proteoforms from they were derived. We here a powerful new strategy identification and elucidation proteoform families (groups related proteoforms) experimental determination accurate number...
The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, writing the sequence of fully characterized proteoforms. ProForma provides means to communicate any proteoform by amino acid using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain acids. is unambiguous, human-readable, can easily be parsed written bioinformatic tools. This system uses seven rules supports wide range possible use...
Post-translationally spliced peptides have recently garnered significant interest as potential targets for cancer immunotherapy and contributors to autoimmune diseases such type 1 diabetes, yet feasible identification methods be developed. Here we present Neo-Fusion, a search program discovering in tandem mass spectrometry data. Neo-Fusion utilizes two separated ion database searches identify the halves of each peptide, then it infers full sequence. This strategy allows without peptide...
Peptides detected by tandem mass spectrometry (MS/MS) in bottom-up proteomics serve as proxies for the proteins expressed sample. Protein inference is a process routinely applied to these peptides generate plausible list of candidate protein identifications. The use multiple proteases parallel digestions expands sequence coverage, provides additional peptide identifications, and increases probability identifying that are unique single protein, which all valuable inference. We have developed...