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:

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

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...
Airborne observations from four flights during the 2008 Indirect and Semi-Direct Aerosol Campaign (ISDAC) are used to examine some cloud-free optical...
The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes....
Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the...
Matrix metalloproteinase enzymes, overexpressed in HT-1080 human fibrocarcinoma tumors, were used to guide the accumulation and retention of an...

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.

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

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

Diffusion in biofilms respiring on electrodes.

Abstract: 

The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed for noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensional De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that (1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; (2) Drs at a given location decreases with G. sulfurreducens biofilm age; (3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and (4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.

Citation: 
Renslow RS, JT Babauta, PD Majors, and H Beyenal.2013."Diffusion in biofilms respiring on electrodes."Energy and Environmental Science 6(2):595-607. doi:10.1039/C2EE23394K
Authors: 
RS Renslow
JT Babauta
PD Majors
H Beyenal
Volume: 
6
Issue: 
2
Pages: 
595-607
Publication year: 
2013

An Interactive Visual Analytics Framework for Multi-Field Data in a Geo-Spatial Context.

Abstract: 

Climate research produces a wealth of multivariate data. These data often have a geospatial reference and so it is of interest to show them within their geospatial context. One can consider this configuration as a multi field visualization problem, where the geospace provides the expanse of the field. However, there is a limit on the amount of multivariate information that can be fit within a certain spatial location, and the use of linked multivari ate information displays has previously been devised to bridge this gap. In this paper we focus on the interactions in the geographical display, present an implementation that uses Google Earth, and demonstrate it within a tightly linked parallel coordinates display. Several other visual representations, such as pie and bar charts are integrated into the Google Earth display and can be interactively manipulated. Further, we also demonstrate new brushing and visualization techniques for parallel coordinates, such as fixedwindow brushing and correlationenhanced display. We conceived our system with a team of climate researchers, who already made a few important discov eries using it. This demonstrates our system’s great potential to enable scientific discoveries, possibly also in oth er domains where data have a geospatial reference.

Citation: 
Zhang Z, X Tong, KT McDonnell, A Zelenyuk, D Imre, and K Mueller.2013."An Interactive Visual Analytics Framework for Multi-Field Data in a Geo-Spatial Context."Tsinghua Science and Technology 18(2):111-124.
Authors: 
Z Zhang
X Tong
KT McDonnell
A Zelenyuk
D Imre
K Mueller
Instruments: 
Volume: 
18
Issue: 
2
Pages: 
111-124
Publication year: 
2013

The Role of Reducible Oxide-Metal Cluster Charge Transfer in Catalytic Processes: New Insights on The Catalytic Mechanism of CO

Abstract: 

To probe metal particle/reducible oxide interactions Density Functional Theory based Ab Initio Molecular Dynamics studies were performed on a prototypical metal cluster (Au20) supported on reducible oxides (rutile TiO2(110)) to implicitly account for finite temperature effects and the role of excess surface charge in the metal oxide. It was found that the charge state of the Au particle is negative in a reducing chemical environment whereas in the presence of oxidizing species co-adsorbed to the oxide surface the cluster obtained a net positive charge. In the context of the well known CO oxidation reaction, charge transfer facilitates the plasticization of Au20 which allows for a strong adsorbate induced surface reconstruction upon addition of CO leading to the formation of mobile Au-CO species on the surface. The charging/discharging of the cluster during the catalytic cycle of CO oxidation enhances and controls the amount of O2 adsorbed at oxide surface/cluster interface and strongly influences the energetics of all redox steps in catalytic conversions. A detailed comparison of the current findings with previous studies is presented and generalities about the role of surface-adsorbate charge transfer for metal cluster/reducible oxide interactions are discussed.

Citation: 
Wang Y, Y Yoon, VA Glezakou, J Li, and RJ Rousseau.2013."The Role of Reducible Oxide-Metal Cluster Charge Transfer in Catalytic Processes: New Insights on The Catalytic Mechanism of CO Oxidation on Au/TiO2 from Ab Initio Molecular Dynamics."Journal of the American Chemical Society 135(29):10673-10683. doi:10.1021/ja402063v
Authors: 
Y Wang
Y Yoon
VA Glezakou
J Li
RJ Rousseau
Instruments: 
Volume: 
135
Issue: 
29
Pages: 
10673-10683
Publication year: 
2013

A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling.

Abstract: 

Although the Euclidean distance does well in measuring data distances within high-dimensional clusters, it does poorly when it comes to gauging inter-cluster distances. This significantly impacts the quality of global, low-dimensional space embedding procedures such as the popular multi-dimensional scaling (MDS) where one can often observe non-intuitive layouts. We were inspired by the perceptual processes evoked in the method of parallel coordinates which enables users to visually aggregate the data by the patterns the polylines exhibit across the dimension axes. We call the path of such a polyline its structure and suggest a metric that captures this structure directly in high-dimensional space. This allows us to better gauge the distances of spatially distant data constellations and so achieve data aggregations in MDS plots that are more cognizant of existing high-dimensional structure similarities. Our MDS plots also exhibit similar visual relationships as the method of parallel coordinates which is often used alongside to visualize the high-dimensional data in raw form. We then cast our metric into a bi-scale framework which distinguishes far-distances from near-distances. The coarser scale uses the structural similarity metric to separate data aggregates obtained by prior classification or clustering, while the finer scale employs the appropriate Euclidean distance.

Citation: 
Lee HJ, KT McDonnell, A Zelenyuk, D Imre, and K Mueller.2014."A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling."IEEE Transactions on Visualization and Computer Graphics 20(3):351-364. doi:10.1109/TVCG.2013.101
Authors: 
HJ Lee
KT McDonnell
A Zelenyuk
D Imre
K Mueller
Instruments: 
Volume: 
20
Issue: 
3
Pages: 
351-364
Publication year: 
2014

Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry.

Abstract: 

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is an imperative goal for the field of medicine. While mass spectrometry (MS)-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry (IMS) separations [1, 2] with liquid chromatography (LC) and MS to dramatically increase measurement sensitivity and throughput, further enabling future MS-based clinical applications. An initial application of the LC-IMS-MS platform for the analysis of blood serum samples from stratified post-liver transplant patients with recurrent fibrosis progression illustrates its potential utility for disease characterization and use in personalized medicine [3, 4].

Citation: 
Baker ES, KE Burnum-Johnson, JM Jacobs, DL Diamond, RN Brown, YM Ibrahim, DJ Orton, PD Piehowski, DE Purdy, RJ Moore, WF Danielson, III, ME Monroe, KL Crowell, GW Slysz, MA Gritsenko, JD Sandoval, BL Lamarche, MM Matzke, BJM Webb-Robertson, BC Simons, BJ McMahon, R Bhattacharya, JD Perkins, RL Carithers, S Strom, S Self, MG Katze, GA Anderson, and RD Smith.2014."Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry."Molecular and Cellular Proteomics 13(4):1119-1127. doi:10.1074/mcp.M113.034595
Authors: 
ES Baker
KE Burnum-Johnson
JM Jacobs
DL Diamond
RN Brown
YM Ibrahim
DJ Orton
PD Piehowski
DE Purdy
RJ Moore
WF Danielson
III
ME Monroe
KL Crowell
GW Slysz
MA Gritsenko
JD Soval
BL Lamarche
MM Matzke
BJM Webb-Robertson
BC Simons
BJ McMahon
R Bhattacharya
JD Perkins
RL Carithers
S Strom
S Self
MG Katze
GA Anderson
RD Smith
Capabilities: 
Volume: 
13
Issue: 
4
Pages: 
1119-1127
Publication year: 
2014

Pages