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

The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse...
The scalable synthesis of subnanometer metal clusters containing an exact number of atoms is of interest due to the highly size-dependent catalytic,...
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...
High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral...

Science Highlights

Posted: December 16, 2014
The Science Microbial communities respond to environmental perturbations through changes in the relative abundance of community members as well as...
Posted: November 20, 2014
The Science All eukaryotes have three essential DNA-dependent RNA polymerase enzymes. These enzymes control gene activity by constructing chains of...
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...

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:

Investigating the Synthesis of Ligated Metal Clusters in Solution Using a Flow Reactor and Electrospray Ionization Mass

Abstract: 

The scalable synthesis of subnanometer metal clusters containing an exact number of atoms is of interest due to the highly size-dependent catalytic, electronic and optical properties of these species. While significant research has been conducted on the batch preparation of clusters through reduction synthesis in solution, the processes of metal complex reduction as well as cluster nucleation, growth and post-reduction etching are still not well understood. Herein, we demonstrate a temperature-controlled flow reactor for studying cluster formation in solution at well-defined conditions. Employing this technique methanol solutions of a chloro(triphenylphosphine)gold precursor, 1,4-bis(diphenylphosphino)butane capping ligand and borane-tert-butylamine reducing agent were combined in a mixing tee and introduced into a heated capillary with an adjustable length. In this manner, the temperature dependence of the relative abundance of different ionic reactants, intermediates and products synthesized in real time was characterized using online mass spectrometry. A wide distribution of doubly and triply charged cationic gold clusters was observed as well as smaller singly charged metal-ligand complexes. The results demonstrate that temperature plays a crucial role in determining the relative population of cationic gold clusters and, in general, that higher temperature promotes the formation of doubly charged clusters and singly charged metal-ligand complexes while hindering the growth of triply charged clusters. Moreover, the distribution of clusters observed at elevated temperatures is found to be consistent with that obtained at longer reaction times at room temperature, thereby demonstrating that heating may be used to access cluster distributions characteristic of different stages of reduction synthesis in solution.

Citation: 
Olivares AM, J Laskin, and GE Johnson.2014."Investigating the Synthesis of Ligated Metal Clusters in Solution Using a Flow Reactor and Electrospray Ionization Mass Spectrometry."Journal of Physical Chemistry A 118(37):8464-8470. doi:10.1021/jp501809r
Authors: 
AM Olivares
J Laskin
GE Johnson
Facility: 
Volume: 
118
Issue: 
37
Pages: 
8464-8470
Publication year: 
2014

Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions.

Abstract: 

The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

Citation: 
Johnson GE, TA Priest, and J Laskin.2014."Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions."Chemical Science 5:3275-3286. doi:10.1039/c4sc00849a
Authors: 
GE Johnson
TA Priest
J Laskin
Facility: 
Volume: 
Issue: 
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Publication year: 
2014

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: 
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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: 
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Publication year: 
2014

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