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.

Additonal Information:

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

Description

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)

 

Instruments

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

Publications

Protein markers for identification of Y. pestis and their variation related to culture
We report on ab initio molecular dynamics simulations of Ca-rich montmorillonite systems, in different hydration states in the presence of...
The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5&...
High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral...
The size and thickness of organic aerosol particles collected by impaction in five field campaigns were compared to those of laboratory generated...

Science Highlights

Posted: September 22, 2014
Phototrophs are organisms that use sunlight to convert inorganic materials to organic materials. Researchers are studying these organisms’...
Posted: September 17, 2014
The Science Oxygen-minimum zones (OMZ) are widespread and naturally occurring oceanographic features. These zones are caused by microbial...
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 post-translationally...

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.

Additonal Information:

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

Protein markers for identification of Yersinia pestis and their variation related to culture.

Abstract: 

Protein markers for identification of Y. pestis and their variation related to culture

Citation: 
Wunschel DS, HE Engelmann, KD Victry, BH Clowers, CM Sorensen, NB Valentine, CM Mahoney Fahey, TW Wietsma, and KL Wahl.2014."Protein markers for identification of Yersinia pestis and their variation related to culture."Molecular and Cellular Probes 28(2-3):65-72. doi:10.1016/j.mcp.2013.12.001
Authors: 
DS Wunschel
HE Engelmann
KD Victry
BH Clowers
CM Sorensen
NB Valentine
CM Mahoney Fahey
TW Wietsma
KL Wahl
Volume: 
28
Issue: 
Pages: 
65-72
Publication year: 
2014

Microstructural Response of Variably Hydrated Ca-Rich Montmorillonite to Supercritical CO2.

Abstract: 

We report on ab initio molecular dynamics simulations of Ca-rich montmorillonite systems, in different hydration states in the presence of supercritical CO2. Analysis of the molecular trajectories provides estimates of the relative H2O:CO2 ratio per interspatial cation. The vibrational density of states in direct comparison with dipole moment derived IR spectra for these systems provide unique signatures that can used to follow molecular transformation. In a co-sequestration scenario, these signatures could be used to identify the chemical state and fate of Sulfur compounds. Interpretation of CO2 asymmetric stretch shift is given based on a detailed analysis of scCO2 structure and intermolecular interactions of the intercalated species. Based on our simulations, smectites with higher charge interlayer cations at sub-single to single hydration states should be more efficient in capturing CO2, while maintaining caprock integrity. This research would not have been possible without the support of the office of Fossil Energy, Department of Energy. The computational resources were made available through a user proposal of the EMSL User facility, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Citation: 
Lee MS, BP McGrail, and VA Glezakou.2014."Microstructural Response of Variably Hydrated Ca-Rich Montmorillonite to Supercritical CO2."Environmental Science & Technology 48(15):8612-8619. doi:10.1021/es5005889
Authors: 
MS Lee
BP McGrail
VA Glezakou
Instruments: 
Volume: 
48
Issue: 
15
Pages: 
8612-8619
Publication year: 
2014

Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs.

Abstract: 

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521.

Citation: 
Parenteau MN, LL Jahnke, JD Farmer, and SL Cady.2014."Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs."Astrobiology 14(6):, doi:10.1089/ast.2013.1122
Authors: 
MN Parenteau
LL Jahnke
JD Farmer
SL Cady
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol.

Abstract: 

The size and thickness of organic aerosol particles collected by impaction in five field campaigns were compared to those of laboratory generated secondary organic aerosols (SOA). Scanning transmission x-ray microscopy (STXM) was used to measure the total carbon absorbance (TCA) by individual particles as a function of their projection areas on the substrate. Because they flatten less upon impaction, particles with higher viscosity and surface tension can be identified by a steeper slope on a plot of TCA vs. size. The slopes of the ambient data are statistically similar indicating a small range of average viscosities and surface tensions across five field campaigns. Steeper slopes were observed for the plots corresponding to ambient particles, while smaller slopes were indicative of the laboratory generated SOA. This comparison indicates that ambient organic particles have higher viscosities and surface tensions than those typically generated in laboratory SOA studies.

Citation: 
O'Brien RE, A Neu, SA Epstein, A MacMillan, B Wang, ST Kelly, S Nizkorodov, A Laskin, RC Moffet, and MK Gilles.2014."Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol."Geophysical Research Letters 41(2):4347-4353. doi:10.1002/2014GL060219
Authors: 
RE O'Brien
A Neu
SA Epstein
A MacMillan
B Wang
ST Kelly
S Nizkorodov
A Laskin
RC Moffet
MK Gilles
Facility: 
Volume: 
41
Issue: 
2
Pages: 
4347-4353
Publication year: 
2014

Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams.

Abstract: 

High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification.

Citation: 
Debord JD, DF Smith, CR Anderton, RM Heeren, L Pasa-Tolic, RH Gomer, and FA Fernandez-Lima.2014."Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams."PLoS One 9(6):e99319. doi:10.1371/journal.pone.0099319
Authors: 
JD Debord
DF Smith
CR Anderton
RM Heeren
L Pasa-Tolic
RH Gomer
FA Fernez-Lima
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Optical, physical, and chemical properties of springtime aerosol over Barrow Alaska in 2008.

Abstract: 

Airborne observations from four flights during the 2008 Indirect and Semi-Direct Aerosol Campaign (ISDAC) are used to examine some cloud-free optical, physical, and chemical properties of aerosol particles in the springtime Arctic troposphere. The number concentrations of particles larger than 0.12 μm (Na>120), important for light extinction and cloud droplet formation, ranged from 15 to 2260 cm−3, with the higher Na>120 cases dominated by measurements from two flights of long-range transported biomass burning (BB) aerosols. The two other flights examined here document a relatively clean aerosol and an Arctic Haze aerosol impacted by larger particles largely composed of dust. For observations from the cleaner case and the BB cases, the particle light scattering coefficients at low relative humidity (RH<20%) increased nonlinearly with increasing Na>120, driven mostly by an increase in mean sizes of particles with increasing Na>120 (BB cases). For those three cases, particle light absorption coefficients also increased nonlinearly with increasing Na>120 and linearly with increasing submicron particle volume concentration. In addition to black carbon, brown carbon was estimated to have increased light absorption coefficients by 27% (450 nm wavelength) and 14% (550 nm) in the BB cases. For the case with strong dust influence, the absorption relative to submicron particle volume was small compared with the other cases. There was a slight gradient of Passive Cavity Aerosol Spectrometer Probe (PCASP) mean volume diameter (MVD) towards smaller sizes with increasing height, which suggests more scavenging of the more elevated particles, consistent with a typically longer lifetime of particles higher in the atmosphere. However, in approximately 10% of the cases, the MVD increased (>0.4 μm) with increasing altitude, suggesting transport of larger fine particle mass (possibly coarse particle mass) at high levels over the Arctic. This may be because of transport of larger particles at higher elevations and relatively slow deposition to the surface.

Citation: 
Shantz NC, I Gultepe, E Andrews, A Zelenyuk, M Earle, AM MacDonald, PS Liu, and WR Leaitch.2014."Optical, physical, and chemical properties of springtime aerosol over Barrow Alaska in 2008."International Journal of Climatology 34(10):3125-3138. doi:10.1002/joc.3898
Authors: 
NC Shantz
I Gultepe
E Andrews
A Zelenyuk
M Earle
AM MacDonald
PS Liu
WR Leaitch
Instruments: 
Volume: 
34
Issue: 
10
Pages: 
3125-3138
Publication year: 
2014

Angular Distribution and Recoil Effect for 1 MeV Au+ Ions through a Si3N4 Thin Foil .

Abstract: 

The Stopping and Range of Ions in Matter (SRIM) code has been widely used to predict nuclear stopping power and angular distribution of ion-solid collisions. However, experimental validation of the predictions is insufficient for slow heavy ions in nonmetallic compounds. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) is applied to determine the angular distribution of 1 MeV Au ions after penetrating a Si3N4 foil with a thickness of ~100 nm. The exiting Au ions are collected by a Si wafer located ~14 mm behind the Si3N4 foil, and the resulting 2-dimensional distribution of Au ions on the Si wafer is measured by ToF-SIMS. The SRIM-predicted angular distribution of Au ions through the Si3N4 thin foil is compared with the measured results, indicating that SRIM slightly overestimates the nuclear stopping power by up to 10%. In addition, thickness reduction of the suspended Si3N4 foils induced by 1 MeV Au ion irradiation is observed with an average loss rate of ~107 atom/ion.

Citation: 
Jin K, Z Zhu, S Manandhar, J Liu, CH Chen, V Shutthanandan, S Thevuthasan, WJ Weber, and Y Zhang.2014."Angular Distribution and Recoil Effect for 1 MeV Au+ Ions through a Si3N4 Thin Foil ."Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 332:346-350. doi:10.1016/j.nimb.2014.02.093
Authors: 
K Jin
Z Zhu
S Manhar
J Liu
CH Chen
V Shutthanan
S Thevuthasan
WJ Weber
Y Zhang
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study.

Abstract: 

Methanol synthesis from CO2 hydrogenation on Pd4/In2O3 has been investigated using density functional theory (DFT) and microkinetic modeling. In this study, three possible routes in the reaction network of CO2 + H2 → CH3OH + H2O have been examined. Our DFT results show that the HCOO route competes with the RWGS route whereas a high activation barrier kinetically blocks the HCOOH route. DFT results also suggest that H2COO* + H* ↔ H2CO* +OH* and cis-COOH* + H* ↔CO* + H2O* are the rate limiting steps in the HCOO route and the RWGS route, respectively. Microkinetic modeling results demonstrate that the HCOO route is the dominant reaction route for methanol synthesis from CO2 hydrogenation. We found that the activation of H adatom on the small Pd cluster and the presence of H2O on the In2O3 substrate play important roles in promoting the methanol synthesis. The hydroxyl adsorbed at the interface of Pd4/In2O3 induces the transformation of the supported Pd4 cluster from a butterfly structure into a tetrahedron structure. This important structure change not only indicates the dynamical nature of the supported nanoparticle catalyst structure during the reaction but also shifts the final hydrogenation step from H2COH to CH3O.

Citation: 
Ye J, C Liu, D Mei, and Q Ge.2014."Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study."Journal of Catalysis 317:44-53. doi:10.1016/j.jcat.2014.06.002
Authors: 
Ye J
C Liu
D Mei
Q Ge
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Enzyme-Directed Assembly of Nanoparticles in Tumors Monitored by In Vivo Whole Animal and Ex Vivo Super-Resolution Fluorescence

Abstract: 

Matrix metalloproteinase enzymes, overexpressed in HT-1080 human fibrocarcinoma tumors, were used to guide the accumulation and retention of an enzyme-responsive nanoparticle in a xenograft mouse model. The nanoparticles were prepared as micelles from amphiphilic block copolymers bearing a simple hydrophobic block, and a hydrophilic peptide brush. The polymers were end-labeled with Alexa Fluor 647 dyes leading to the formation of labeled micelles upon dialysis of the polymers from DMSO to aqueous buffer. This dye-labeling strategy allowed the presence of the retained material to be visualized via whole animal imaging in vivo, and in ex vivo organ analysis following intratumoral injection into HT-1080 xenograft tumors. We propose that the material is retained by virtue of an enzyme-induced accumulation process whereby particles change morphology from 20 nm spherical micelles to micron-scale aggregates, kinetically trapping them within the tumor. This hypothesis is tested here via an unprecedented super resolution fluorescence analysis of ex vivo tissue slices confirming a particle size increase occurs concomitantly with extended retention of responsive particles compared to unresponsive controls.

Citation: 
Chien MP, AS Carlini, D Hu, CV Barback, AM Rush, DJ Hall, G Orr, and NC Gianneschi.2013."Enzyme-Directed Assembly of Nanoparticles in Tumors Monitored by In Vivo Whole Animal and Ex Vivo Super-Resolution Fluorescence Imaging."Journal of the American Chemical Society 135(50):18710-18713. doi:10.1021/ja408182p
Authors: 
MP Chien
AS Carlini
D Hu
CV Barback
AM Rush
DJ Hall
G Orr
NC Gianneschi
Facility: 
Instruments: 
Volume: 
135
Issue: 
50
Pages: 
18710-18713
Publication year: 
2013

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