A5063058293- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Bioinformatics and Genomic Networks
- Analytical Chemistry and Chromatography
- Microbial Community Ecology and Physiology
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Analytical chemistry methods development
- Cytomegalovirus and herpesvirus research
- Hippo pathway signaling and YAP/TAZ
- Protein Structure and Dynamics
- Scientific Computing and Data Management
- Microfluidic and Capillary Electrophoresis Applications
- RNA and protein synthesis mechanisms
- Hydrocarbon exploration and reservoir analysis
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Microbial Fuel Cells and Bioremediation
- Legionella and Acanthamoeba research
- Identification and Quantification in Food
- Cellular transport and secretion
- Solar and Space Plasma Dynamics
- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- Geophysics and Gravity Measurements
Environmental Molecular Sciences Laboratory
2001-2024
Pacific Northwest National Laboratory
2001-2015
Oregon Health & Science University
2004-2009
Dartmouth College
2009
Argonne National Laboratory
2005
National Institutes of Health
2005
National Center for Biotechnology Information
2005
Princeton University
2004
University of Alabama at Birmingham
2004
Blood serum is a complex body fluid that contains various proteins ranging in concentration over at least 9 orders of magnitude. Using combination mass spectrometry technologies with improvements sample preparation, we have performed proteomic analysis submilliliter quantities and increased the measurable range for blood beyond previous reports. We detected 490 by on-line reversed-phase microcapillary liquid chromatography coupled ion trap spectrometry. To perform this analysis,...
ABSTRACT Human cytomegalovirus (HCMV), a member of the herpesvirus family, is large complex enveloped virus composed both viral and cellular gene products. While sequence HCMV genome has been known for over decade, full set proteins that compose virion are unknown. To approach this problem we have utilized gel-free two-dimensional capillary liquid chromatography-tandem mass spectrometry (MS/MS) Fourier transform ion cyclotron resonance MS to identify determine relative abundances in purified...
The use of artificial neural networks (ANNs) is described for predicting the reversed-phase liquid chromatography retention times peptides enzymatically digested from proteome-wide proteins. To enable accurate comparison numerous LC/MS data sets, a genetic algorithm was developed to normalize peptide into range (from 0 1), improving elution time reproducibility ∼1%. network in this study based on amino acid residue composition and consists 20 input nodes, 2 hidden 1 output node. A set ∼7000...
Abstract Summary: DeconMSn accurately determines the monoisotopic mass and charge state of parent ions from high-resolution tandem spectrometry data, offering significant improvement for LTQ_FT LTQ_Orbitrap instruments over commercially delivered Thermo Fisher Scientific's extract_msn tool. Optimal ion tolerance values can be determined using accurate information, thus improving peptide identifications high-mass measurement accuracy experiments. For low-resolution data LCQ LTQ instruments,...
The γ-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, ≈40% the predicted ORFs in S. genome were annotated as uncharacterized “hypothetical” genes. We implemented an integrative approach by using experimental computational analyses provide more detailed insight into gene function. Global expression profiles determined for cells...
Neurite extension and growth cone navigation are guided by extracellular cues that control cytoskeletal rearrangements. However, understanding the complex signaling mechanisms mediate neuritogenesis has been limited inability to biochemically separate neurite soma for spatial proteomic bioinformatic analyses. Here, we apply global proteome profiling in combination with a purification methodology comparative analysis of proteomes neuroblastoma cells. The relationship 4,855 proteins were...
While comparative bacterial genomic studies commonly predict a set of genes indicative common ancestry, experimental validation the existence this core genome requires extensive measurement and is typically not undertaken. Enabled by an proteome database developed over six years, we have experimentally verified expression proteins predicted from ortholog comparisons among 17 environmental pathogenic bacteria. More exclusive relationships were observed expressed protein content phenotypically...
Recent multidimensional liquid chromatography MS/MS studies have contributed to the identification of large numbers expressed proteins for numerous species. The present study couples size exclusion intact with separation tryptically digested peptides using a combination strong cation exchange and high resolution, reversed phase capillary identify extracted from human mammary epithelial cells (HMECs). In addition conventional conservative criteria protein identifications, confidence levels...
Abstract Characterization of the human blood plasma proteome is critical to discovery routinely useful clinical biomarkers. We used an accurate mass and time (AMT) tag strategy with high‐resolution accuracy cLC‐FT‐ICR MS perform a global proteomic analysis pilot study samples as part HUPO Plasma Proteome Project. reference serum citrated from African Americans, Asian Caucasian Americans were analyzed, in addition Pacific Northwest National Laboratory plasma. The AMT allowed us leverage two...
Using stringent criteria for protein identification by accurate mass and time (AMT) tag spectrometric methodology, we detected 36 proteins of <101 amino acids in length, including 10 that were annotated as hypothetical proteins, 172 global tryptic digests Shewanella oneidensis MR-1 proteins. Peptides map to the conserved, but functionally uncharacterized SO4134 SO2787, most frequently peptides these samples, while those hypotheticals SO2669 SO2063, conserved SO0335 SO2176, SlyX (SO1063)...
The dynamic range of Fourier transform ion cyclotron mass spectrometry (FTICR) is typically limited by the useful charge capacity an FTICR cell (to ∼106 to 107 elementary charges) and minimum number ions required produce a signal (∼102 charges). We show that expansion 2 orders magnitude can be achieved preselecting lower abundance species in quadrupole interface electrospray ionization (ESI) source. Ion preselection then followed accumulation external linear (2-D) trap subsequent transfer...
We evaluate statistical models used in two-hypothesis tests for identifying peptides from tandem mass spectrometry data. The null hypothesis H0, that a peptide matches spectrum by chance, requires information on the probability of by-chance between fragments and peaks spectrum. Likewise, alternate HA, is due to particular peptide, probabilities would indeed be observed if it was causative agent. compare these determining identification rates produced using an independent data set. initial...
We successfully modified an existing method to investigate protein−protein interactions in the pathogenic bacterium Salmonella enterica serovar Typhimurium (Salmonella Typhimurium). This includes (i) addition of a histidine-biotin-histidine tag bait proteins via recombinant DNA techniques, (ii) vivo cross-linking with formaldehyde, (iii) tandem affinity purification under fully denaturing conditions, and (iv) identification cross-linked by liquid-chromatography conjunction mass-spectrometry....
The Software Environment for Biological Network Inference (SEBINI) has been created to provide an interactive environment the deployment and testing of network inference algorithms that use high-throughput expression data. Networks inferred from SEBINI software platform can be further analyzed using Collective Analysis Interaction (CABIN), allows integration analysis protein- protein interaction gene-to-gene regulatory evidence obtained multiple sources. In this paper, we present a case...
We present a platform for the reconstruction of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey data. The Software Environment Biological Network Inference (SEBINI), an environment deployment network inference algorithms that use high-throughput data, forms core. Among many available in SEBINI is Bayesian Estimator Probabilities Protein-Protein Associations (BEPro3) algorithm, which used to infer such MS affinity isolation Also, pipeline incorporates...
An Adaptable Multiple Power Source (AMPS) system has been designed and constructed. The AMPS can provide up to 16 direct current (DC) (±400 V; 5 mA), 4 radio frequency (RF) (two 500 VPP sinusoidal signals each, 0.5-5 MHz) channels, 2 high voltage sources (±6 kV), one ∼40 W, 250 °C temperature-regulated heater. is controlled by a microcontroller, capable of communicating with its front panel or computer. It assign not only pre-saved fixed DC RF but also profiled voltages. driving many mass...