A5065424710- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Machine Learning in Bioinformatics
- Block Copolymer Self-Assembly
- Glycosylation and Glycoproteins Research
- Protein purification and stability
- Protein Structure and Dynamics
- Theoretical and Computational Physics
- Metabolomics and Mass Spectrometry Studies
- Material Dynamics and Properties
- Genomics and Phylogenetic Studies
- Fluid Dynamics and Thin Films
- Rheology and Fluid Dynamics Studies
- Surfactants and Colloidal Systems
- Spectroscopy Techniques in Biomedical and Chemical Research
- RNA and protein synthesis mechanisms
- Peptidase Inhibition and Analysis
- Force Microscopy Techniques and Applications
- Adhesion, Friction, and Surface Interactions
- Polymer Surface Interaction Studies
- Polymer crystallization and properties
- Viral Infectious Diseases and Gene Expression in Insects
- Microfluidic and Capillary Electrophoresis Applications
- Spectroscopy and Quantum Chemical Studies
- Biosimilars and Bioanalytical Methods
Protein Metrics (United States)
2015-2021
Agilent Technologies (United States)
2010
University of Chicago
1995-2000
School of the Art Institute of Chicago
1996
The Paragon™ Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using sequence tag algorithm, allowing degree implication by an MS/MS spectrum each region to be determined on continuum. Counter conventional approaches, features such as modifications, substitutions, and cleavage events modeled with probabilities rather than discrete user-controlled settings consider or not...
Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With rapid advances mass technology methods, it has become imperative to provide standard output format data that will facilitate sharing analysis. Initially, efforts develop resulted multiple formats, each designed with different underlying philosophy. To resolve issues associated having vendors, researchers, software developers convened under banner of HUPO PSI single standard. The new incorporated...
False discovery rate (FDR) analyses of protein and peptide identification results using decoy database searching conventionally report aggregate or global FDRs for a whole set identifications, which are often not very informative about the error rates individual members in set. We describe nonlinear curve fitting method calculating local FDR, estimates chance that an (or peptide) is incorrect, present simple tool implements this analysis. The goal to offer extension now commonplace...
Charge deconvolution infers the mass from over charge (m/z) measurements in electrospray ionization spectra. When applied a wide input m/z or broad target range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half one-third of correct mass. Indeed, maximum entropy term objective function MaxEnt, most commonly used algorithm, favors deconvolved spectrum with many peaks one fewer peaks. Here we describe new "parsimonious" algorithm that produces artifacts....
Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides with smaller posttranslational modifications. Exact structural elucidation glycans is generally the capability single mass spectrometry experiment, so reasonable level identification for tandem spectrometry, taken several glycopeptide software tools, that sequence glycan composition, meaning monosaccharides each distinct mass, e.g.,...
We present an MS/MS database search algorithm with the following novel features: (1) a protein structure containing extensive preindexing and (2) zone modification searching, which enables rapid discovery of modifications known (i.e., user-specified) unanticipated delta masses. All these features are implemented in Interrogator, engine that runs behind Pro ID, ICAT, QUANT software products. Speed benchmarks demonstrate our modification-tolerant is 100-fold faster than traditional algorithms...
Applications of antibody de novo sequencing in the biopharmaceutical industry range from discovery new drug candidates to identifying reagents for research and determining primary structure innovator products biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target interest are available, but cDNA original cell line is not, protein required humanize recombinantly express these antibodies, followed by vitro vivo testing functional...
With the increased development of new RNA-based therapeutics, need for robust analytical methods confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed nucleotides, thus hampering complete sequence coverage confident localization modifications. Ultraviolet photodissociation (UVPD) shown great potential characterization nucleic due to extensive backbone...
We study symmetric and nearly diblock copolymers confined to thin films of thickness L, where L is the equilibrium bulk lamellar period. The film surfaces have opposite preferences for polymer species; this results in frustration. use Scheutjens−Fleer method calculate free energies several parallel (with respect surfaces), perpendicular, mixed perpendicular morphologies as a function preferential wetting strengths species at surfaces. When surface highly preferential, morphology adopts novel...
We studied the effect of monomer immobilization (quenching) on orientation lamellae in symmetric diblock copolymer thin films with neutrally wetting surfaces. A small fraction monomers immediately next to solid substrate is presumed be quenched. Our calculations demonstrate that quenching favors orienting perpendicular film. Quenching inhibits order−disorder transition twice as much for parallel orientation.
We develop methods for alleviating the major impediment in extension to larger and more complex systems of our matrix method theory describing long time dynamics flexible polymers proteins solution. This is associated with enormous growth size required basis set addition higher order mode coupling functions, which are needed describe influence on ‘‘internal friction,’’ or equivalently memory function matrices. use first eigenfunctions (the generalized Rouse modes) construct an approximate...
Mass spectrometry is gaining momentum as a method of choice to de novo sequence antibodies (Abs). Adequate coverage the hypervariable regions remains one toughest identification challenges by either bottom‐up or top‐down workflows. Methods that efficiently generate mid‐size Ab fragments would further facilitate MS and decrease data complexity. Here, we explore proteases Cathepsins L D for forming protein from three IgG1s, IgG2, bispecific, knob‐and‐hole IgG1. We demonstrate high‐resolution...
We investigate bridging in a telechelic polymer brush solution using the Milner−Witten−Cates self-consistent mean-field model. For an uncompressed between flat, parallel plates, equilibrium number of bridges is predicted to be proportional (R/L0)2, where R root-mean-square end-to-end distance and L0 height. Upon compressing this system, much higher form. moderate compression − L such that ξ ≪ ≲ L0/2, interpenetration depth two opposing brushes, (L0 L)(R/L0)2/3. Changing geometry system from...
We extend to nonequilibrium processes our recent theory for the long time dynamics of flexible chain molecules. While previous describes equilibrium motions any bond or interatomic separation in (bio)polymers by correlation functions, present extension enables prediction relaxation that occurs processes, such as T-jump experiments, where there are sudden transitions between, example, different states. As a test theory, we consider ``unfolding'' pentadecane when it is transported from...