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.

A new state-of-the-art 21T FTICR mass spectrometer will be online this summer. To learn more about this system, the science it will advance, and its historical development, visit the 21T HRMAC webpage.

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
This instrument is housed in EMSL.  More information about this instrument will be available soon.
EMSL’s 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer, or 21T FTICR MS, is one of only two in the world with this high of a...
Custodian(s): Ljiljana Pasa-Tolic
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

Metal reduction capability has been found in numerous species of environmentally abundant Gram-positive bacteria. However, understanding of microbial...
Interrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in...
A significant fraction of atmospheric organic compounds is predominantly found in condensed phases, such as aerosol particles and cloud droplets....
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring...
We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study on the measurement of composition in...

Science Highlights

Posted: February 05, 2016
Fundamental and Applied Reviews in Analytical Chemistry 2016 special issue features a research team known for their expertise in ambient ionization...
Posted: January 26, 2016
Scientists at Pacific Northwest National Laboratory, or PNNL, and Argonne National Laboratory have developed a "vitamin mimic" – a molecule that...
Posted: December 21, 2015
Scientists at Pacific Northwest National Laboratory and Joint BioEnergy Institute used capabilities at EMSL and DOE Joint Genome Institute to study...
Posted: December 16, 2015
The Science Atmospheric brown carbon is generated from a variety of biogenic and anthropogenic emission sources. The carbon absorbs a significant...
Posted: November 10, 2015
Researchers have a new way to characterize materials for carbon sequestration, develop solid catalysts to produce biofuels, optimize food industry...

Instruments

The interaction between plants and their environment is of key importance in promoting sustainable, healthy, and robust plant growth. Underlying the...
The interaction between plants and their environment is of key importance in promoting sustainable, healthy, and robust plant growth. Underlying the...
The microbial activities on which humanity and ecosystems depend are determined by microbial community membership and by the resources and conditions...
Enzymatic hydrolysis of (ligno)cellulose by cellulases is key for the production of second generation biofuels which represent a long-standing...
While nitrogen management is an important agronomic trait in any cropping system, it is of particular concern for future bioenergy crops that will be...

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.

A new state-of-the-art 21T FTICR mass spectrometer will be online this summer. To learn more about this system, the science it will advance, and its historical development, visit the 21T HRMAC webpage.

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

On Surface Order and Disorder of α-Pinene-Derived Secondary Organic Material.

Abstract: 

The surfaces of secondary organic aerosol particles are notoriously difficult to access experimentally, even though they are the key location where exchange between the aerosol particle phase and its gas phase occurs. Here, we overcome this difficulty by applying standard and sub 1-cm-1 resolution vibrational sum frequency generation (SFG) spectroscopy to detect C–H oscillators at the surfaces of secondary organic material (SOM) prepared from the ozonolysis of α-pinene at Harvard University and at the University of California, Irvine that were subsequently collected on Teflon filters as well as CaF2 windows using electrostatic deposition. We find both samples yield comparable SFG spectra featuring an intense peak at 2940 cm-1 that are independent of spectral resolution and location or method of preparation. We hypothesize that the SFG spectra are due to surface-active C–H oscillators associated with the four-membered ring motif of α-pinene, which produces an unresolvable spectral continuum of approximately 50 cm-1 width reminiscent of the similar, albeit much broader, O–H stretching continuum observed in the SFG spectra of aqueous surfaces. Upon subjecting the SOM samples to cycles in relative humidity (RH) between <2% RH and 95% RH, we observe reversible changes in the SFG signal intensity across the entire spectral range surveyed for a polarization combination probing components of the vibrational transition dipole moments that are oriented parallel to the plane of incidence, but no signal intensity changes for any other polarization combination investigated. These results support the notion that the C–H oscillators at the surfaces of α-pinene-derived SOM deposited on CaF2 windows shift back and forth between two different molecular orientation distributions as the RH is lowered (more ordered) or raised (less ordered). The findings thus point towards the presence of a reversible surface switch for hindering (more ordered, <2%RH) and promoting (less ordered, 95%RH) exchange between the aerosol particle phase and its gas phase.

Citation: 
Shrestha M, Y Zhang, MA Upshur, P Liu, SL Blair, H Wang, S Nizkorodov, R Thomson, ST Martin, and FM Geiger.2015."On Surface Order and Disorder of ?-Pinene-Derived Secondary Organic Material."Journal of Physical Chemistry A 119(19):4609-4617. doi:10.1021/jp510780e
Authors: 
Wang Hongfei
Shrestha M
Y Zhang
MA Upshur
P Liu
SL Blair
H Wang
S Nizkorodov
R Thomson
ST Martin
FM Geiger
Capabilities: 
Facility: 
Volume: 
119
Issue: 
19
Pages: 
4609-4617
Publication year: 
2015

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...