Mass Spectrometry

Systems biology and complex mixture studies in biofuels, microbial communities, climate and environmental remediation can be analyzed with word-class separations and mass spectrometry capabilities.

Resources and Techniques
Panomics - Advanced global proteomics, metabolomics, glycomics and activity-based omics research using cutting-edge tools, including customized hardware and sophisticated bioinformatics tools. This research includes:

  • Confident protein identification and quantitation using stable-isotope labeling and label-free strategies
  • Subcellular localization, turnover rates and modification states of proteins
  • Top-down proteomics and broad intact-protein level measurements
  • Characterization of protein-protein/metabolite interactions
  • Activity based proteomics and other targeted proteomics strategies such as phosphoproteomics and biomarker validation.

Natural Organic Matter - Several workflows targeting different classes of organic compounds in soil and the environment have been developed.

Aerosol Particle Characterization - Real-time data is captured on environmentally relevant aerosols with high specificity and resolution using field-deployable equipment.

Ion-surface Collision - Fundamental aspects of activation, dissociation and deposition (soft-landing) of complex molecular ions are studied following collision with specially prepared surfaces using uniquely configured instrumentation.

Other research resources found in EMSL and managed by Pacific Northwest National Laboratory include:

Proteomics Capabilities

  • High resolution and mass accuracy Fourier-transform ion cyclotron resonance (FT-ICR) spectrometers, from 6 Tesla (T) to 15T and 21T in development
  • Orbitrap based platforms including Elite, Velos and Exactive mass spectrometers
  • Triple-quadrupole mass spectrometers for targeted quantitation
  • Gas Chromatography (GC) MS instruments with extensive compound identification libraries
  • Ion mobility spectrometry (IMS) coupled to time-of-flight (TOF) mass spectrometers
  • Advanced custom nano-HPLC systems, augmented by Agilent, Waters and Eksigent systems
  • MALDI and C60 SIMS mass spectrometry imaging (MSI) ion sources

 Aerosol Capabilities

  • LTQ-Orbitrap
  • Field-deployable, second-generation, single-particle, laser-ablation, TOF mass spectrometer (SPLAT II)
  • Proton transfer reaction mass spectrometer
  • High-resolution TOF aerosol mass spectrometer

Ion-Surface Collision Study Capabilities

  • 6T FT-ICR spectrometer configured for studying ion-surface interactions
  • Ion deposition instrument for preparation of novel materials using ion soft-landing
  • TOF secondary ion mass spectrometer (TOF-SIMS)

 

The Quadrupole Aerosol Mass Spectrometer (QAMS) manufactured by Aerodyne Inc., was added as a capability in the EMSL user facility in 2004 and the...
Custodian(s): M Lizabeth Alexander
The 6-Tesla High-Field Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS), is a unique instrument designed and constructed at...
Custodian(s): Julia Laskin
This high-resolution ICP-MS complements the isotopic capabilities of the Neptune by providing highly accurate and sensitive elemental concentrations...
Custodian(s): M Lizabeth Alexander
The Agilent 4500 Series inductively coupled plasma mass spectrometer (ICP-MS) is available for all research areas requiring analysis of trace metals...
Custodian(s): Tom Wietsma
The Exactive MS provides ultra-high resolution MS capability and will be coupled with elemental/isotopic ion sources to provide truly unique and...
Custodian(s): David Koppenaal
Calculations were performed to determine the structures, energetics, and spectroscopy of the atmospherically relevant complexes (HNO₃)&...
Although it has been shown that size of atmospheric particles has a direct correlation with their ability to act as cloud droplet and ice nuclei, the...
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different...
Bottom-up nanostructure synthesis has played a pivotal role in the advancement of nanoscale science. This approach is typically less labor and energy...
The annotation of protein function is almost completely performed by in silico approaches. However, computational prediction of protein function is...
Posted: August 08, 2014
The Science Technetium-99 is a common radioactive contaminant in groundwater at nuclear waste reprocessing sites and a top priority for remediation...
Posted: August 07, 2014
Scientists at Pacific Northwest National Laboratory and Oregon Health & Science University working at EMSL developed a new technique that...
Posted: June 27, 2014
The Science In the environment, microbes often communicate with each other using small molecules. Ribosomally synthesized and posttranslationally...
Posted: May 26, 2014
Reduction-oxidation, or "redox," regulation is essential for many biological processes in all organisms. To help understand these processes,...
Posted: April 28, 2014
A team of scientists from the University of Missouri, Pacific Northwest National Laboratory and EMSL showed Arabidopsis, a small flowing plant...

Systems biology and complex mixture studies in biofuels, microbial communities, climate and environmental remediation can be analyzed with word-class separations and mass spectrometry capabilities.

Resources and Techniques
Panomics - Advanced global proteomics, metabolomics, glycomics and activity-based omics research using cutting-edge tools, including customized hardware and sophisticated bioinformatics tools. This research includes:

  • Confident protein identification and quantitation using stable-isotope labeling and label-free strategies
  • Subcellular localization, turnover rates and modification states of proteins
  • Top-down proteomics and broad intact-protein level measurements
  • Characterization of protein-protein/metabolite interactions
  • Activity based proteomics and other targeted proteomics strategies such as phosphoproteomics and biomarker validation.

Natural Organic Matter - Several workflows targeting different classes of organic compounds in soil and the environment have been developed.

Aerosol Particle Characterization - Real-time data is captured on environmentally relevant aerosols with high specificity and resolution using field-deployable equipment.

Ion-surface Collision - Fundamental aspects of activation, dissociation and deposition (soft-landing) of complex molecular ions are studied following collision with specially prepared surfaces using uniquely configured instrumentation.

Other research resources found in EMSL and managed by Pacific Northwest National Laboratory include:

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass.

Abstract: 

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the littlestudied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify .3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

Citation: 
D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer.2013."Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass."PLoS One 8(7):e68465. doi:10.1371/journal.pone.0068465
Authors: 
P D'haeseleer
JM Gladden
M Allgaier
P Chain
SG Tringe
S Malfatti
JT Aldrich
CD Nicora
EW Robinson
L Pasa-Tolic
P Hugenholtz
BA Simmons
SW Singer
Facility: 
Publication year: 
2013

Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria.

Abstract: 

To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either aerobic or suboxic conditions. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily caused by differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Altered transcription levels appeared responsible for 26% of the protein changes, altered translational efficiency appeared responsible for 46% and a combination of both were responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part caused by altered tRNA pools, is a major determinant of regulated protein expression in bacteria.

Citation: 
Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley.2013."Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria."Integrative Biology 5(11):1393-1406. doi:10.1039/C3IB40120K
Authors: 
RC Taylor
BJM Webb-Robertson
LM Markillie
MH Serres
BE Linggi
JT Aldrich
EA Hill
MF Romine
MS Lipton
HS Wiley
Facility: 
Volume: 
5
Issue: 
11
Pages: 
1393-1406
Publication year: 
2013

Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions

Abstract: 

Cultures of the cyanobacterial genus Cyanothece have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N2-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes and we performed quantitative proteome analysis of Cyanothece ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N2-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome c oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose-phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in Cyanothece ATCC 51142 in the presence of glycerol under H2 producing conditions, suggesting a competition between these sources of carbon. However, in Cyanothece PCC 7822, the Calvin cycle still played a role in cofactor recycling during H2 production. Our data comprise the first comprehensive profiling of proteome changes in Cyanothece PCC 7822, and allows an in-depth comparative analysis of major physiological and biochemical processes that influence H2-production in both the strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large scale H2 production.

Citation: 
Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman.2013."Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production."Applied and Environmental Microbiology 79(4):1070-1077. doi:10.1128/AEM.02864-12
Authors: 
UK Aryal
SJ Callister
S Mishra
X Zhang
JI Shutthanan
TE Angel
AK Shukla
ME Monroe
RJ Moore
DW Koppenaal
RD Smith
L Sherman
Facility: 
Instruments: 
Volume: 
79
Issue: 
4
Pages: 
1070-1077
Publication year: 
2013

Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface.

Abstract: 

The majority of in vitro studies characterizing the impact of engineered nanoparticles (NPs) on cells that line the respiratory tract were conducted in cells exposed to NPs in suspension. This approach introduces processes that are unlikely to occur during inhaled NP exposures in vivo, such as the shedding of toxic doses of dissolved ions. ZnO NPs are used extensively and pose significant sources for human exposure. Exposures to airborne ZnO NPs can induce adverse effects, but the relevance of the dissolved Zn2+ to the observed effects in vivo is still unclear. Our goal was to mimic in vivo exposures to airborne NPs and decipher the contribution of the intact NP from the contribution of the dissolved ions to airborne ZnO NP toxicity. We established the exposure of alveolar type II epithelial cells to aerosolized NPs at the air-liquid interface (ALI), and compared the impact of aerosolized ZnO NPs and NPs in suspension at the same cellular doses, measured as the number of particles per cell. By evaluating membrane integrity and cell viability 6 and 24 hours post exposure we found that aerosolized NPs induced toxicity at the ALI at doses that were in the same order of magnitude as doses required to induce toxicity in submersed cultures. In addition, distinct patterns of oxidative stress were observed in the two exposure systems. These observations unravel the ability of airborne ZnO NPs to induce toxicity without the contribution of dissolved Zn2+ and suggest distinct mechanisms at the ALI and in submersed cultures.

Citation: 
Xie Y, NG Williams, A Tolic, WB Chrisler, JG Teeguarden, BL Maddux, JG Pounds, A Laskin, and G Orr.2012."Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface."Toxicological Sciences 125(2):450-461. doi:10.1093/toxsci/kfr251
Authors: 
Y Xie
NG Williams
A Tolic
WB Chrisler
JG Teeguarden
BL Maddux
JG Pounds
A Laskin
G Orr
Facility: 
Volume: 
125
Issue: 
2
Pages: 
450-461
Publication year: 
2012

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