A5052412732- Ionosphere and magnetosphere dynamics
- Methane Hydrates and Related Phenomena
- Geophysics and Gravity Measurements
- Earthquake Detection and Analysis
- Seismic Waves and Analysis
- Astrophysics and Cosmic Phenomena
- Solar and Space Plasma Dynamics
- Seismology and Earthquake Studies
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Microbial Community Ecology and Physiology
- Analytical Chemistry and Chromatography
- Marine and coastal ecosystems
- Isotope Analysis in Ecology
- Soil Carbon and Nitrogen Dynamics
- Genomics and Phylogenetic Studies
- Advanced Chemical Sensor Technologies
- Atmospheric chemistry and aerosols
- Peptidase Inhibition and Analysis
- Peatlands and Wetlands Ecology
- Smart Materials for Construction
- Climate change and permafrost
- Agriculture, Soil, Plant Science
- Water Quality Monitoring and Analysis
Environmental Molecular Sciences Laboratory
2015-2024
Pacific Northwest National Laboratory
2015-2024
The Ohio State University
2022
Richland College
2016-2019
Indiana University School of Medicine
2016
Indiana University – Purdue University Indianapolis
2016
University of California, Irvine
2016
Gachon University
2010
Korea University
2010
Korea Institute of Science and Technology
2010
Understanding biological systems and the roles of their constituents is facilitated by ability to make quantitative, sensitive, comprehensive measurements how proteome changes, e.g., in response environmental perturbations. To this end, we have developed a high-throughput methodology characterize an organism's dynamic based on combination global enzymatic digestion, high-resolution liquid chromatographic separations, analysis Fourier transform ion cyclotron resonance mass spectrometry. The...
Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment natural matter (NOM). In this work, we describe software Formularity with a user-friendly interface CIA function and newly search Isotopic Pattern (IPA). While assigns formulas compounds containing C,...
van Krevelen diagrams (O/C vs H/C ratios of elemental formulas) have been widely used in studies to obtain an estimation the main compound categories present environmental samples. However, limits defining a specific category based solely on O/C and formulas never accurately listed or proposed classify metabolites biological Furthermore, while can provide overview categories, such classification is inefficient because large overlap among different along both axes. We propose more accurate...
Soil organic matter (SOM), a complex, heterogeneous mixture of above and belowground plant litter animal microbial residues at various degrees decomposition, is key reservoir for carbon (C) nutrient biogeochemical cycling in soil based ecosystems. A limited understanding the molecular composition SOM limits ability to routinely decipher chemical processes within accurately predict how terrestrial fluxes will respond changing climatic conditions land use. To elucidate molecular-level...
Abstract High‐resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges data comparison and interpretation among laboratories operating instruments with differing performance user conditions. It is therefore essential that the community establishes metric ranges compositional trends reference samples so can be robustly compared research groups. To this end, four identically...
ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTHigh Throughput Proteome-Wide Precision Measurements of Protein Expression Using Mass SpectrometryLjiljana Paša-Tolić, Pamela K. Jensen, Gordon A. Anderson, Mary S. Lipton, Kim Peden, Suzana Martinović, Nikola Tolić, James E. Bruce, and Richard D. SmithView Author Information Environmental Molecular Sciences Laboratory Pacific Northwest National P.O. Box 999, Richland, Washington 99352 Cite this: J. Am. Chem. Soc. 1999, 121, 34,...
Abstract Summary: The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets instrument types. VIPER software package one the key components data processing pipeline implements automated algorithms to discover LC-MS features, align match these features a database peptides previously identified in LC-MS/MS analyses, identify quantify pairs isotopically labeled peptides. Availability: may be downloaded...
We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. The consists (i) chemical cross-linking reaction: intact cell labeling with class cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 PIR-labeled proteins construction restricted database by two-dimensional...
Abstract Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by variety interacting proteins. We report novel online two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) platform for high-throughput sensitive characterization PTMs at the intact protein level. The enables unambiguous identification 708 isoforms from single 2D LC-MS/MS...
Hydroxyl radicals (·OH) exert a strong impact on the carbon cycle due to their nonselective and highly oxidizing nature. Reduced iron-containing clay minerals (RIC) are one of major contributors formation ·OH in dark environments, but interactions with humic acids (HA) poorly known. Here, we investigate mutual between RIC HA under oxygenated conditions. decreased oxidation rate structural Fe(II) significantly promoted yield. dissolved fraction from form an aqueous Fe(II)–HA complex. were...
Secondary organic aerosol (SOA), formed in the photooxidation of diesel fuel, biodiesel and 20% fuel/80% fuel mixture, are prepared under high-NOx conditions presence absence sulfur dioxide (SO2), ammonia (NH3), relative humidity (RH). The composition condensed-phase compounds SOA is measured using several complementary techniques including mass spectrometry (AMS), high-resolution nanospray desorption electrospray ionization (nano-DESI/HRMS), ultrahigh resolution accuracy 21T Fourier...
We provide the initial performance evaluation of a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer operating at Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory. The constructed for 21T system employs commercial dual linear trap coupled to FTICR designed and built in-house. Performance gains from moving higher magnetic field strength are exemplified by measurement peptide isotopic fine structure, complex natural organic matter mixtures,...
Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details these transformations remain unclear. This study reports application ultrahigh resolution mass spectrometry to profile composition SOM and its during simulated warming experiment. A sample, collected near Barrow, Alaska, USA, was subjected 40-day incubation under anoxic conditions analyzed before after determine changes composition. CHO index based on C, H, O...
Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due heterogeneity unknown SOC compositions. Using ultrahigh-resolution mass spectrometry, we determined compositional changes extractable dissolved matter (EDOM) in an anoxic warming incubation experiment (up 122 days) with a tundra from Alaska (United States). EDOM was extracted 10 mM NH4HCO3 both organic- mineral-layer soils during at −2 8 °C. Based on their O:C H:C...
Pilot Project #1--the identification and characterization of human histone H4 proteoforms by top-down MS--is the first project launched Consortium for Top-Down Proteomics (CTDP) to refine validate MS. Within initial results from seven participating laboratories, all reported probability-based (UniProt accession P62805) with expectation values ranging 10(-13) 10(-105). Regarding characterization, a total 74 were reported, 21 done so unambiguously; one new PTM, K79ac, was identified....
Ultrasensitive nanoscale proteomics approaches for characterizing proteins from complex proteomic samples of <50 ng total mass are described. Protein identifications 0.5 pg whole proteome extracts were enabled by ultrahigh sensitivity (<75 zmol individual proteins) achieved using high-efficiency (peak capacities ∼103) 15-μm-i.d. capillary liquid chromatography separations (i.e., nanoLC, ∼20 nL/min mobile-phase flow rate at the optimal linear velocity ∼0.2 cm/s) coupled on-line with a...
We report on the design and application of a high-efficiency multiple-capillary liquid chromatography (LC) system for high-throughput proteome analysis. The LC using commercial pumps was operated at pressure 10 000 psi to deliver mobile phases through novel passive feedback valve arrangement that permitted mobile-phase flow path switching efficient sample introduction. uses several serially connected dual-capillary column devices. approach eliminates time delays regeneration (or...
Chemical cross-linking combined with mass spectrometry can be a powerful approach for the identification of protein−protein interactions and providing constraints on protein structures. However, enrichment cross-linked peptides is crucial to reduce sample complexity before spectrometric analysis. In addition compact cross-linkers are often preferred provide short spacer lengths, surface accessibility complexes, must have reasonable solubility under conditions where native complex structure...
Abstract. Organic aerosol formation and transformation occurs within aqueous cloud droplets, yet little is known about the composition of high molecular weight organic compounds in water. Cloud water samples collected at Whiteface Mountain, New York, during August–September 2014 were analyzed by ultra-high-resolution mass spectrometry to investigate dissolved carbon, with a focus on sulfur- nitrogen-containing compounds. was evaluated context inorganic ion concentrations, pH, total carbon...
The relatively poor solubility of lignin in most pretreatment solvents remains one the biggest challenges valorization to improve overall biorefinery economics.
Abstract Sphagnum mosses dominate peatlands by employing harsh ecosystem tactics to prevent vascular plant growth and microbial degradation of these large carbon stores. Knowledge about ‐produced metabolites, their structure function, is important better understand the mechanisms, underlying this sequestration phenomenon in face climate variability. It currently unclear which compounds are responsible for inhibition organic matter decomposition mechanisms occurs. Metabolite profiling fallax...
Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well the activity of species. The application these ranges from studying microbial communities important for global biogeochemical cycling host-microbiota interactions intestinal tract. Current SIP approaches, such DNA-SIP or nanoSIMS allow analyze incorporation stable isotopes with high coverage taxa community at single cell level, respectively,...