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

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and...
Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of...
Gasoline Compression Ignition (GCI) engines have the potential to achieve high fuel efficiency and to significantly reduce both NOx and particulate...
Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural...
The occurrence of plutonium dioxide (PuO2) either from direct deposition or from the precipitation of plutonium-bearing solutions in contaminated...

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...

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:

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO.

Abstract: 

Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a
single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed a+b fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.

Citation: 
Eletsky A, K Michalska, S Houliston, Q Zhang, MD Daily, X Xu, H Cui, A Yee, A Lemak, B Wu, M Garcia, MC Burnet, KM Meyer, UK Aryal, O Sanchez, C Ansong, R Xiao, T Acton, JN Adkins, G Montelione, A Joachimiak, CH Arrowsmith, A Savchenko, T Szyperski, and JR Cort.2014."Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO."PLoS One 9(7):Article No. e101787. doi:10.1371/journal.pone.0101787
Authors: 
A Eletsky
K Michalska
S Houliston
Q Zhang
MD Daily
X Xu
H Cui
A Yee
A Lemak
B Wu
M Garcia
MC Burnet
KM Meyer
UK Aryal
O Sanchez
C Ansong
R Xiao
T Acton
JN Adkins
G Montelione
A Joachimiak
CH Arrowsmith
A Savchenko
T Szyperski
JR Cort
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations.

Abstract: 

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

Citation: 
Pierce EM, P Frugier, LJ Criscenti, KD Kwon, and SN Kerisit.2014."Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations."International Journal of Applied Glass Science 5(4):421-435. doi:10.1111/ijag.12077
Authors: 
EM Pierce
P Frugier
LJ Criscenti
KD Kwon
SN Kerisit
Volume: 
5
Issue: 
4
Pages: 
421-435
Publication year: 
2014

Automated genome mining of ribosomal peptide natural products.

Abstract: 

Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic datasets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs and apply it for lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connection of multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 as the first natural product to be identified in an automated fashion by genome mining. The presented tool is available at cy-clo.ucsd.edu.

Citation: 
Mohimani H, R Kersten, W Liu, M Wang, SO Purvine, S Wu, HM Brewer, L Pasa-Tolic, N Bandeira, BS Moore, PA Pevzner, and PC Dorrestein.2014."Automated genome mining of ribosomal peptide natural products."ACS Chemical Biology 9(7):1545-1551. doi:10.1021/cb500199h
Authors: 
H Mohimani
R Kersten
W Liu
M Wang
SO Purvine
S Wu
HM Brewer
L Pasa-Tolic
N Beira
BS Moore
PA Pevzner
PC Dorrestein
Instruments: 
Volume: 
9
Issue: 
7
Pages: 
1545-1551
Publication year: 
2014

Detailed Characterization of Particulates Emitted by Pre-Commercial Single-Cylinder Gasoline Compression Ignition Engine.

Abstract: 

Gasoline Compression Ignition (GCI) engines have the potential to achieve high fuel efficiency and to significantly reduce both NOx and particulate matter (PM) emissions by operating under dilute partially-premixed conditions. This low temperature combustion strategy is dependent upon direct-injection of gasoline during the compression stroke and potentially near top dead center (TDC). The timing and duration of the in-cylinder injections can be tailored based on speed and load to create optimized conditions that result in a stable combustion. We present the results of advanced aerosol analysis methods that have been used for detailed real-time characterization of PM emitted from a single-cylinder GCI engine operated at different speed, load, timing, and number and duration of near-TDC fuel injections. PM characterization included 28 measurements of size and composition of individual particles sampled directly from the exhaust and after mass and/or mobility classification. We use these data to calculate particle effective density, fractal dimension, dynamic shape factors in free-molecular and transition flow regimes, average diameter of primary spherules, number of spherules, and void fraction of soot agglomerates.

Citation: 
Zelenyuk A, P Reitz, ML Stewart, D Imre, P Loeper, C Adams, M Andrie, D Rothamer, DE Foster, K Narayanaswamy, PM Najt, and AS Solomon.2014."Detailed Characterization of Particulates Emitted by Pre-Commercial Single-Cylinder Gasoline Compression Ignition Engine."Combustion and Flame 161(8):2151-2164. doi:10.1016/j.combustflame.2014.01.011
Authors: 
A Zelenyuk
P Reitz
ML Stewart
D Imre
P Loeper
C Adams
M Andrie
D Rothamer
DE Foster
K Narayanaswamy
PM Najt
AS Solomon
Volume: 
161
Issue: 
8
Pages: 
2151-2164
Publication year: 
2014

Yeast cell surface display for lipase whole cell catalyst and its applications.

Abstract: 

The cell surface display technique allows for the expression of target proteins or peptides on the microbial cell surface by fusing an appropriate protein as an anchoring motif. Yeast display systems, such as Pichia pastoris, Yarowia lipolytica and Saccharomyces cerevisiae, are ideal, alternative and extensive display systems with the advantage of simple genetic manipulation and post-translational modification of expressed heterologous proteins. Engineered yeasts show high performance characteristics and variant utilizations. Herein, we comprehensively summarize the variant factors affecting lipase whole cell catalyst activity and display efficiency, including the structure and size of target proteins, screening anchor proteins, type and chain length of linkers, and the appropriate matching rules among the above-mentioned display units. Furthermore, we also address novel approaches to enhance stability and activity of recombinant lipases, such as VHb gene co-expression, multi-enzyme co-display technique, and the micro-environmental interference and self-assembly techniques. Finally, we represent the variety of applications of whole cell surface displayed lipases on yeast cells in non-aqueous phases, including synthesis of esters, PUFA enrichment, resolution of chiral drugs, organic synthesis and biofuels. We demonstrate that the lipase surface display technique is a powerful tool for functionalizing yeasts to serve as whole cell catalysts, and increasing interest is providing an impetus for broad application of this technique.

Citation: 
Liu Y, R Zhang, Z Lian, S Wang, and AT Wright.2014."Yeast cell surface display for lipase whole cell catalyst and its applications."Journal of Molecular Catalysis B: Enzymatic 106:17-25. doi:10.1016/j.molcatb.2014.04.011
Authors: 
Y Liu
R Zhang
Z Lian
S Wang
AT Wright
Volume: 
Issue: 
Pages: 
Publication year: 
2014

In-situ Study of Nanostructure and Electrical Resistance of Nanocluster Films Irradiated with Ion Beams.

Abstract: 

An in-situ study is reported on the structural evolution in nanocluster films under He+ ion irradiation using an advanced helium ion microscope. The films consist of loosely interconnected nanoclusters of magnetite or iron-magnetite (Fe-Fe3O4) core-shells. The nanostructure is observed to undergo dramatic changes under ion-beam irradiation, featuring grain growth, phase transition, particle aggregation, and formation of nanowire-like network and nano-pores. Studies based on ion irradiation, thermal annealing and election irradiation have indicated that the major structural evolution is activated by elastic nuclear collisions, while both electronic and thermal processes can play a significant role once the evolution starts. The electrical resistance of the Fe-Fe3O4 films measured in situ exhibits a super-exponential decay with dose. The behavior suggests that the nanocluster films possess an intrinsic merit for development of an advanced online monitor for neutron radiation with both high detection sensitivity and long-term applicability, which can enhance safety measures in many nuclear operations.

Citation: 
Jiang W, JA Sundararajan, T Varga, ME Bowden, Y Qiang, JS McCloy, CH Henager, Jr, and RO Montgomery.2014."In-situ Study of Nanostructure and Electrical Resistance of Nanocluster Films Irradiated with Ion Beams."Advanced Functional Materials 24(39):6210-6218. doi:10.1002/adfm.201400553
Authors: 
W Jiang
JA Sundararajan
T Varga
ME Bowden
Y Qiang
JS McCloy
CH Henager
Jr
RO Montgomery
Instruments: 
Volume: 
24
Issue: 
39
Pages: 
6210-6218
Publication year: 
2014

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

Abstract: 

Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.

Citation: 
Hawley AK, HM Brewer, AD Norbeck, L Pasa-Tolic, and SJ Hallam.2014."Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes."Proceedings of the National Academy of Sciences of the United States of America 111(31):11395-11400. doi:10.1073/pnas.1322132111
Authors: 
AK Hawley
HM Brewer
AD Norbeck
L Pasa-Tolic
SJ Hallam
Volume: 
111
Issue: 
31
Pages: 
11395-11400
Publication year: 
2014

Characterization of Defects in N-type 4H-SiC After High-Energy N Ion Implantation by RBS-Channeling and Raman Spectroscopy.

Abstract: 

Implantation with 1 MeV N ions was performed at room temperature in n-type 4H-SiC(0001) to four implantation fluences (or doses in dpa (displacements per atom) at the damage peak) of 1.5×1013(0.0034), 7.8×1013(0.018), 1.5×1014(0.034), and 7.8×1014(0.18) ions/cm2, respectively. The evolution of disorder was studied using Rutherford backscattering spectrometry in channeling mode (RBS-C) and Raman spectroscopy. The disorder in the Si sub-lattice was found to be less than 10% for the dpa of 0.0034 and 0.0178 and increased to 40% and 60% for the dpa of 0.034 and 0.178 respectively. Raman Spectroscopy was performed using a green laser of wavelength 532 nm as excitation source. The normalized Raman Intensity, In shows disorder of 41%, 69%, 77% and 100% for the dpa of 0.0034, 0.017, 0.034 and 0.178 respectively. In this paper, the characterizations of the defects produced due to the Nitrogen implantation in 4H-SiC are presented and the results are discussed.

Citation: 
Kummari VC, T Reinert, W Jiang, FD McDaniel, and B Rout.2014."Characterization of Defects in N-type 4H-SiC After High-Energy N Ion Implantation by RBS-Channeling and Raman Spectroscopy."Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 332:28-32. doi:10.1016/j.nimb.2014.02.023
Authors: 
VC Kummari
T Reinert
W Jiang
FD McDaniel
B Rout
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation.

Abstract: 

Leaf-cutter ants are dominant herbivores in ecosystems throughout the Neotropics. Rather than directly consuming the fresh foliar biomass they harvest, these ants use it to cultivate specialized fungus gardens. Although recent investigations have shed light on how plant biomass is degraded in fungus gardens, the cycling of nutrients that takes place in these specialized microbial ecosystems is still not well understood. Here, using metametabolomics and metaproteomics techniques, we examine the dynamics of nutrient turnover and biosynthesis in these gardens. Our results reveal that numerous free amino acids and sugars are depleted throughout the process of biomass degradation, indicating that easily accessible nutrients from plant material are readily consumed by microbes in these ecosystems. Accumulation of cellobiose and lignin derivatives near the end of the degradation process is consistent with previous findings of cellulases and laccases produced by Leucoagaricus gongylophorus, the fungus cultivated by leaf-cutter ants. Our results also suggest that ureides may be an important source of nitrogen in fungus gardens, especially during nitrogen-limiting conditions. No free arginine was detected in our metametabolomics experiments despite evidence that the host ants cannot produce this amino acid, suggesting that biosynthesis of this metabolite may be tightly regulated in the fungus garden. These results provide new insights into the dynamics of nutrient cycling that underlie this important ant-fungus symbiosis.

Citation: 
Huang EL, FO Aylward, YM Kim, BJM Webb-Robertson, CD Nicora, Z Hu, TO Metz, MS Lipton, RD Smith, CR Currie, and KE Burnum-Johnson.2014."The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation."Environmental Microbiology Reports 6(4):389-95. doi:10.1111/1758-2229.12163
Authors: 
EL Huang
FO Aylward
YM Kim
BJM Webb-Robertson
CD Nicora
Z Hu
TO Metz
MS Lipton
RD Smith
CR Currie
KE Burnum-Johnson
Volume: 
6
Issue: 
4
Pages: 
389-95
Publication year: 
2014

Pages