A5050302903- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Advanced Biosensing Techniques and Applications
- Genomics and Phylogenetic Studies
- Muscle metabolism and nutrition
- Immune cells in cancer
- Adipose Tissue and Metabolism
- Autophagy in Disease and Therapy
- Bioinformatics and Genomic Networks
- Microbial Fuel Cells and Bioremediation
- Exercise and Physiological Responses
- Epigenetics and DNA Methylation
- Axon Guidance and Neuronal Signaling
- Radioactive element chemistry and processing
- Nuclear Structure and Function
- Biotin and Related Studies
- Drug Transport and Resistance Mechanisms
- Sulfur Compounds in Biology
- Metal Extraction and Bioleaching
- Seismology and Earthquake Studies
- Genomics and Chromatin Dynamics
- Advanced Neuroimaging Techniques and Applications
- Methane Hydrates and Related Phenomena
- Iron oxide chemistry and applications
IQE (United Kingdom)
2024
Harvard University
2014-2020
Harvard Stem Cell Institute
2019
BioWorks (United States)
2018
Pfizer (United States)
2018
Dana-Farber Cancer Institute
2017
United States Geological Survey
2016
Oak Ridge National Laboratory
2008-2013
University of Tennessee at Knoxville
2008-2011
Lawrence Livermore National Laboratory
2010
Multiplexed quantitation via isobaric chemical tags (e.g., tandem mass (TMT) and for relative absolute (iTRAQ)) has the potential to revolutionize quantitative proteomics. However, until recently utility of these was questionable due reporter ion ratio distortion resulting from fragmentation coisolated interfering species. These signals can be negated through additional gas-phase manipulations MS/MS/MS (MS3) proton-transfer reactions (PTR)). methods, however, have a significant sensitivity...
Artificial human gut microbial communities implanted into germ-free mice provide insights how species-level responses to changes in diet give rise community-level structural and functional reconfiguration types of bacteria prioritize use available nutrients vivo.
Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude workflows have been developed for multiplexed analyses, the most quantitatively accurate method (SPS-MS3) suffers from long acquisition duty cycles. We built new, real-time database search (RTS) platform, Orbiter, to combat SPS-MS3 method's longer RTS with Orbiter eliminates scans if no peptide matches given spectrum. With Orbiter's online proteomic analytical pipeline, which includes and...
As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create new paradigm quantitative proteomics. New instrumentation software are propelling these workflows forward, which results more accurate, sensitive, reproducible across tens thousands phosphopeptides. This study assesses performance phosphoproteomics on Orbitrap Fusion mass...
Brown adipose tissue (BAT) mitochondria exhibit high oxidative capacity and abundant expression of both electron transport chain components uncoupling protein 1 (UCP1). UCP1 dissipates the mitochondrial proton motive force (Δp) generated by respiratory increases thermogenesis. Here we find that in mice genetically lacking UCP1, cold-induced activation metabolism triggers innate immune signaling markers cell death BAT. Moreover, global proteomic analysis reveals this cascade induced deletion...
Quantitative proteomics employing isobaric reagents has been established as a powerful tool for biological discovery. Current workflows often utilize dedicated quantitative spectrum to improve accuracy and precision. A consequence of this approach is dramatic reduction in the spectral acquisition rate, which necessitates use additional instrument time achieve comprehensive proteomic depth. This work assesses performance benefits online real-time identification multiplexed workflows....
Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration mass spectrometry-based data with computational proteome environmental metagenomic sequences has been challenging because the variable overlap between proteomic datasets and corresponding short-read nucleotide In this study, we have benchmarked several strategies for increasing...
Abstract Neurofilament light (NfL) concentration in cerebrospinal fluid (CSF) and blood serves as an important biomarker neurology drug development. Changes NfL are generally assumed to reflect changes neuronal damage, while little is known about the clearance of from biofluids. We observed increase 3.5-fold plasma 5.7-fold CSF asymptomatic individual at risk for genetic prion disease following 6 weeks’ treatment with oral minocycline a dermatologic indication. Other biomarkers remained...
Isobaric labeling strategies for mass spectrometry-based proteomics enable multiplexed simultaneous quantification of samples and therefore substantially increase the sample throughput in proteomics. However, despite these benefits, current limits to multiplexing capacity are prohibitive large sizes impose limitations on experimental design. Here, we introduce a novel mechanism increasing density isobaric reagents. We present Combinatorial Mass Tags (CMTs), an architecture with unique...
<h2>Abstract</h2> Nitrate (NO<sub>3</sub><sup>−</sup>) and nitrite (NO<sub>2</sub><sup>−</sup>) are known to be cardioprotective alter energy metabolism <i>in vivo</i>. NO<sub>3</sub><sup>−</sup> action results from its conversion NO<sub>2</sub><sup>−</sup> by salivary bacteria, but the mechanism(s) which affects remains obscure. may act <i>S</i>-nitrosating protein thiols, thereby altering activity. But how this occurs, functional importance of <i>S</i>-nitrosation sites across mammalian...
Targeted protein quantification using liquid chromatography–tandem mass spectrometry with stable isotope-labeled standards is recognized as the gold standard of practice for quantification. Such assays, however, can only cover a limited number proteins, and developing targeted methods larger numbers proteins requires substantial investment. Alternatively, large-scale global proteomic experiments along computational such "total approach" (TPA) have potential to provide extensive In this...
Many methods of microbial proteome characterizations require large quantities cellular biomass (>1−2 g) for sample preparation and protein identification. Our experimental approach differs from traditional techniques by providing the ability to identify proteomic state a microbe few milligrams starting material. The small-scale, guanidine lysis method minimizes loss achieving digestion in single-tube experiment. For this approach, freshwater Shewanella oneidensis MR-1 purple non-sulfur...
Current state-of-the-art experimental and computational proteomic approaches were integrated to obtain a comprehensive protein profile of Populus vascular tissue. This featured: (1) large sample set consisting two genotypes grown under normal tension stress conditions, (2) bioinformatics clustering effectively handle gene duplication, (3) an informatics approach track identify single amino acid polymorphisms (SAAPs). By applying algorithm the database, number entries decreased from 64,689...
First posted August 18, 2016 For additional information, contact: Director, Geologic Hazards Science CenterU.S. Geological SurveyBox 25046, MS 966Denver, CO 80225-0046http://geohazards.cr.usgs.gov/ This report provides an overview of the capabilities and design Hydra, global seismic monitoring analysis system used for earthquake response catalog production at U.S. Survey National Earthquake Information Center (NEIC). Hydra supports NEIC’s worldwide mission in areas such as event detection,...
Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide sample multiplexing. TOMAHAQ assays enable sensitive accurate multiplexed quantification implementing an intricate data collection scheme comprises multiple MSn scans, mass inclusion lists, data-driven filters. Consequently, manual creation of methods can be time-consuming error prone, while the resulting may not...
Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core gene
An integrated computational/experimental approach was used to predict and identify signal peptide cleavages among microbial proteins of environmental biofilm communities growing in acid mine drainage (AMD). SignalP-3.0 employed computationally query the AMD protein database >16,000 proteins, which resulted 1,480 predicted cleaved proteins. LC−MS/MS analyses extracellular (secretome) preparations from different locations developmental states empirically confirmed 531 these The majority...