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. See a complete list of Mass Spectrometry instruments.

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 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 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
The Neptune is a mid-resolution, multi-collector ICP-MS instrument capable of simultaneous collection of up to nine elemental/isotopic masses,...
Custodian(s): M Lizabeth Alexander
Nano-DESI/HRMS analytical platform allows in-depth molecular characterization of very small samples of organic materials  (down to 10 ng) and...
Custodian(s): Alexander Laskin
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

Publications

Fusions between the transmembrane protease serine 2 (TMPRSS2) and ETS related gene (ERG) represent one of the most specific biomarkers that define a...
Grain growth of nanocrystalline materials is generally thermally activated, but can also be driven by irradiation at much lower temperature. In...
14YWT oxide dispersion strengthened (ODS) ferritic steel was irradiated with of 5 MeV Ni2+ ions, at 300 °C, 450 °C, and 600 °...
Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-...
The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the...

Science Highlights

Posted: February 20, 2015
The Science Secondary organic aerosol (SOA) particles represent a major component of atmospheric particulates and are known to affect climate, air...
Posted: February 06, 2015
The Science Cyanobacteria are of considerable interest as production organisms in biotechnology. They can grow by harvesting energy from sunlight,...
Posted: January 12, 2015
Sea spray particles in the atmosphere can become coated with human-made and natural carbon-rich chemicals causing them to evolve, according to...
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...

Instruments

There are no related projects at this time.

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. See a complete list of Mass Spectrometry instruments.

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:

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

Abstract: 

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases are presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.

Citation: 
Wang Z, K Jin, Y Zhang, F Wang, and Z Zhu.2014."ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?"Surface and Interface Analysis 46(S1):257-260. doi:10.1002/sia.5419
Authors: 
Z Wang
K Jin
Y Zhang
F Wang
Z Zhu
Volume: 
46
Issue: 
0
Pages: 
257-260
Publication year: 
2014

Stability Of Nanoclusters In 14YWT Oxide Dispersion Strengthened Steel Under Heavy Ion-irradiation By Atom Probe Tomography.

Abstract: 

14YWT oxide dispersion strengthened (ODS) ferritic steel was irradiated with of 5 MeV Ni2+ ions, at 300 °C, 450 °C, and 600 °C to a damage level of 100 dpa. The stability of Ti–Y–O nanoclusters was investigated by applying atom probe tomography (APT) in voltage mode, of the samples before and after irradiations. The average size and number density of the nanoclusters was determined using the maximum separation method. These techniques allowed for the imaging of nanoclusters to sizes well below the resolution limit of conventional transmission electron microscopy techniques. The most significant changes were observed for samples irradiated at 300 °C where the size (average Guinier radius) and number density of nanoclusters were observed to decrease from 1.1 nm to 0.8 nm and 12 × 1023 to 3.6 × 1023, respectively. In this study, the nanoclusters are more stable at higher temperature.

Citation: 
He J, F Wan, K Sridharan, TR Allen, AG Certain, V Shutthanandan, and Y Wu.2014."Stability Of Nanoclusters In 14YWT Oxide Dispersion Strengthened Steel Under Heavy Ion-irradiation By Atom Probe Tomography."Journal of Nuclear Materials 455(1-3):41-45. doi:10.1016/j.jnucmat.2014.03.024
Authors: 
He J
F Wan
K Sridharan
TR Allen
AG Certain
V Shutthanan
Y Wu
Instruments: 
Volume: 
455
Issue: 
0
Pages: 
41-45
Publication year: 
2014

The Effect of Eectronic Energy Loss on Irradiation-Induced Grain Growth in Nanocrystalline Oxides.

Abstract: 

Grain growth of nanocrystalline materials is generally thermally activated, but can also be driven by irradiation at much lower temperature. In nanocrystalline ceria and zirconia, contributions from both displacement damage and ionization to the grain growth are identified. Our atomistic simulations have revealed fast grain boundary (GB) movements due to the high density of disorder near GBs. Our experimental results have shown that irradiation-induced grain growth is a function of total energy deposited, where the excitation of target electrons and displacement of lattice atoms both contribute to the overall disorder and both play important roles in grain growth. The coupling of energy deposition to the electronic and lattice structures should both be taken into consideration when engineering nanostructural materials.

Citation: 
Zhang Y, DS Aidhy, T Varga, S Moll, PD Edmondson, F Namavar, K Jin, CN Ostrouchov, and WJ Weber.2014."The Effect of Eectronic Energy Loss on Irradiation-Induced Grain Growth in Nanocrystalline Oxides."Physical Chemistry Chemical Physics. PCCP 16(17):8051-8059. doi:10.1039/c4cp00392f
Authors: 
Y Zhang
DS Aidhy
T Varga
S Moll
PD Edmondson
F Namavar
K Jin
CN Ostrouchov
WJ Weber
Volume: 
16
Issue: 
17
Pages: 
8051-8059
Publication year: 
2014

Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer.

Abstract: 

Fusions between the transmembrane protease serine 2 (TMPRSS2) and ETS related gene (ERG) represent one of the most specific biomarkers that define a distinct molecular subtype of prostate cancer. The studies on TMPRSS2-ERG gene fusions have seldom been performed at the protein level, primarily due to the lack of high-quality antibodies or an antibody-independent method that is sufficiently sensitive for detecting the truncated ERG protein products resulting from TMPRSS2-ERG gene fusions and alternative splicing. Herein, we applied a recently developed PRISM (high-pressure high-resolution separations with intelligent selection and multiplexing)-SRM (selected reaction monitoring) strategy for quantifying ERG protein in prostate cancer cell lines and tumors. The highly sensitive PRISM-SRM assays led to confident detection of 6 unique ERG peptides in either the TMPRSS2-ERG positive cell lines or tissues but not in the negative controls, indicating that ERG protein expression is highly correlated with TMPRSS2-ERG gene rearrangements. Significantly, our results demonstrated for the first time that at least two groups of ERG protein isoforms were simultaneously expressed at variable levels in TMPRSS2-ERG positive samples as evidenced by concomitant detection of two mutually exclusive peptides. Three peptides shared across almost all fusion protein products were determined to be the most abundant peptides, and hence can be used as “signature” peptides for detecting ERG overexpression resulting from TMPRSS2-ERG gene fusion. These PRISM-SRM assays provide valuable tools for studying TMPRSS2-ERG gene fusion protein products, thus improving our understanding of the role of TMPRSS2-ERG gene fusion in the biology of prostate cancer.

Citation: 
He J, X Sun, T Shi, AA Schepmoes, TL Fillmore, VA Petyuk, F Xie, R Zhao, MA Gritsenko, F Yang, N Kitabayashi, SS Chae, M Rubin, J Siddiqui, J Wei, AM Chinnaiyan, W Qian, RD Smith, J Kagan, S Srivastava, KD Rodland, T Liu, and DG Camp, II.2014."Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer."Molecular Oncology 8(7):1169-1180. doi:10.1016/j.molonc.2014.02.004
Authors: 
He J
X Sun
T Shi
AA Schepmoes
TL Fillmore
VA Petyuk
F Xie
R Zhao
MA Gritsenko
F Yang
N Kitabayashi
SS Chae
M Rubin
J Siddiqui
J Wei
AM Chinnaiyan
W Qian
RD Smith
J Kagan
S Srivastava
KD Rodl
T Liu
DG Camp
II
Capabilities: 
Volume: 
8
Issue: 
7
Pages: 
1169-1180
Publication year: 
2014

Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania donovani .

Abstract: 

The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment. However, little is known about the molecular mechanisms underlying the parasite response to environmental changes, such as nutrient availability. To elucidate nutrient stress response pathways in Leishmania donovani, we have used purine starvation as the paradigm. The salvage of purines from the host milieu is obligatory for parasite replication; nevertheless, purine-starved parasites can persist in culture without supplementary purine for over 3 months, indicating that the response to purine starvation is robust and engenders parasite survival under conditions of extreme scarcity. To understand metabolic reprogramming during purine starvation we have employed global approaches. Whole proteome comparisons between purine-starved and purine-replete parasites over a 6-48 h span have revealed a temporal and coordinated response to purine starvation. Purine transporters and enzymes involved in acquisition at the cell surface are upregulated within a few hours of purine removal from the media, while other key purine salvage components are upregulated later in the time-course and more modestly. After 48 h, the proteome of purine-starved parasites is extensively remodeled and adaptations to purine stress appear tailored to deal with both purine deprivation and general stress. To probe the molecular mechanisms affecting proteome remodeling in response to purine starvation, comparative RNA-seq analyses, qRT-PCR, and luciferase reporter assays were performed on purine-starved versus purine-replete parasites. While the regulation of a minority of proteins tracked with changes at the mRNA level, for many regulated proteins it appears that proteome remodeling during purine stress occurs primarily via translational and/or post-translational mechanisms.

Citation: 
Martin JL, PA Yates, R Soysa, JF Alfaro, F Yang, KE Burnum-Johnson, VA Petyuk, KK Weitz, DG Camp, II, RD Smith, PA Wilmarth, LL David, G Ramasamy, PJ Myler, and NS Carter.2014."Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania donovani ."PLoS Pathogens 10(2):e1003938. doi:10.1371/journal.ppat.1003938
Authors: 
JL Martin
PA Yates
R Soysa
JF Alfaro
F Yang
KE Burnum-Johnson
VA Petyuk
KK Weitz
DG Camp
II
RD Smith
PA Wilmarth
LL David
G Ramasamy
PJ Myler
NS Carter
Capabilities: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater.

Abstract: 

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a major benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.

Citation: 
Wang YC, DK Schreiber, JJ Neeway, S Thevuthasan, JE Evans, JV Ryan, Z Zhu, and W Wei.2014."NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater."Surface and Interface Analysis 46(S1):233-237. doi:10.1002/sia.5585
Authors: 
YC Wang
DK Schreiber
JJ Neeway
S Thevuthasan
JE Evans
JV Ryan
Z Zhu
W Wei
Volume: 
46
Issue: 
Pages: 
233-237
Publication year: 
2014

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy.

Abstract: 

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate efficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localization patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells.

Citation: 
Gunsolus IL, D Hu, C Mihai, SE Lohse, CS Lee, M Torelli, RJ Hamers, C Murphy, G Orr, and CL Haynes.2014."Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy."Analyst 139(12):3174-3178. doi:10.1039/c4an00574k
Authors: 
IL Gunsolus
D Hu
C Mihai
SE Lohse
CS Lee
M Torelli
RJ Hamers
C Murphy
G Orr
CL Haynes
Facility: 
Volume: 
139
Issue: 
12
Pages: 
3174-3178
Publication year: 
2014

Microstructure and Cs Behavior of Ba-Doped Aluminosilicate Pollucite Irradiated with F+ Ions.

Abstract: 

Radionuclide 137Cs is one of the major fission products that dominate heat generation in spent fuels over the first 300 hundred years. A durable waste form for 137Cs that decays to 137Ba is needed to minimize its environmental impact. Aluminosilicate pollucite CsAlSi2O6 is selected as a model waste form to study the decay-induced structural effects. While Ba-containing precipitates are not present in charge-balanced Cs0.9Ba0.05AlSi2O6, they are found in Cs0.9Ba0.1AlSi2O6 and identified as monoclinic Ba2Si3O8. Pollucite is susceptible to electron irradiation induced amorphization. The threshold density of the electronic energy deposition for amorphization is determined to be ~235 keV/nm3. Pollucite can be readily amorphized under F+ ion irradiation at 673 K. A significant amount of Cs diffusion and release from the amorphized pollucite is observed during the irradiation. However, cesium is immobile in the crystalline structure under He+ ion irradiation at room temperature. The critical temperature for amorphization is not higher than 873 K under F+ ion irradiation. If kept at or above 873 K all the time, the pollucite structure is unlikely to be amorphized; Cs diffusion and release are improbable. A general discussion regarding pollucite as a potential waste form is provided in this report.

Citation: 
Jiang W, L Kovarik, Z Zhu, T Varga, MH Engelhard, ME Bowden, TM Nenoff, and T Garino.2014."Microstructure and Cs Behavior of Ba-Doped Aluminosilicate Pollucite Irradiated with F+ Ions."Journal of Physical Chemistry C 118(31):18160-18169. doi:10.1021/jp5045223
Authors: 
W Jiang
L Kovarik
Z Zhu
T Varga
MH Engelhard
ME Bowden
TM Nenoff
T Garino
Instruments: 
Volume: 
118
Issue: 
31
Pages: 
18160-18169
Publication year: 
2014

Surface Plasmon-Driven Water Reduction: Gold Nanoparticle Size Matters.

Abstract: 

Water reduction under two visible light ranges (λ > 400 and λ > 435 nm) was investigated using gold-loaded titanium dioxide (Au-TiO2) with different sizes of Au nanoparticles (NPs). Two different mechanisms have been determined to clarify the specific role of Au NPs in visible light-induced photocatalytic reactions. Our study provides solid evidences showing that Au NPs sizes are essential for the surface plasmon-driven water reduction under λ > 435 nm. More specifically, we have demonstrated that the Au NPs sizes are vital for the SPR mediated electron transfer efficiency and play a critical role in determining the reduction potential of the transferred electrons in the TiO2 conduction band (CB) and their following activities. Our discovery provides a facile way to manipulate the reduction potential of transferred electrons by simply varying the Au NPs sizes, which will greatly facilitate the design of suitable plasmonic photocatalysts for water reduction and other valuable solar-to-fuel reactions.

Citation: 
Qian K, BC Sweeny, AC Johnston-Peck, W Niu, JO Graham, JS DuChene, J Qiu, YC Wang, MH Engelhard, D Su, EA Stach, and W Wei.2014."Surface Plasmon-Driven Water Reduction: Gold Nanoparticle Size Matters."Journal of the American Chemical Society 136(28):9842-9845. doi:10.1021/ja504097v
Authors: 
K Qian
BC Sweeny
AC Johnston-Peck
W Niu
JO Graham
JS DuChene
J Qiu
YC Wang
MH Engelhard
D Su
EA Stach
W Wei
Instruments: 
Volume: 
136
Issue: 
28
Pages: 
9842-9845
Publication year: 
2014

Pages

Leads

(509) 371-6341

As part of the EMSL mission, his major projects include implementing the next generation state-of-the-art mass spectrometry instrumentation for biological systems analysis such as the recently completed EMSL capital investment projects funded by...