Office of Science

Mass Spectrometry

EMSL's mass spectrometry capabilities enable high-throughput, high-resolution analysis of complex mixtures. These resources are applied to a broad range of scientific problems from proteomics studies with applications to human health and environmental remediation to aerosol particle characterization, as well as fundamental studies of ion-surface collisions and preparatory mass spectrometry using ion soft-landing.

Proteomics Resources and Research

Proteomics capabilities housed in EMSL, including state-of-the-art instruments and sophisticated bioinformatics methods, have been developed and acquired in coordination with the EMSL scientific user program and Pacific Northwest National Laboratory (PNNL) programmatic research. These resources may be accessed via EMSL User Access or by collaborating with scientists who perform proteomics research at PNNL.

Cutting-edge proteomics tools and methods available at EMSL facilitate advanced global proteomics research and allow detailed visualization and analyses of cellular proteins. Proteomics research and tools at EMSL include:

Photo of staff in Lab

Though access to mass spectrometry hardware at EMSL is only available to EMSL users and PNNL collaborators, PNNL and EMSL provide a collection of software tools to the entire proteomics community through the National Center for Research Resources Proteomics Research Resource for Integrative Biology, such as the PC-based software package, DECON2LS, and VIPER, which offers 'omics data analysis capabilities. Software and data can also be accessed via Biological and Environmental Research – PNNL Proteomics and PNNL's Biological MS Data and Software Distribution Center.

Aerosol Particle Characterization Resources and Research

Unique, state-of-the-art mass spectrometry tools enable EMSL users to characterize environmentally relevant aerosols with high specificity and resolution. Scientists use these tools to study fast chemical reactions; characterize particles with low number concentrations; detect and characterize the chemical structure of high-molecular weight organic compounds in aerosol and cloud water samples; and characterize in detail the chemical composition and transformation of particulate matter collected on substrates using novel atmospheric pressure surface ionization techniques.

Many EMSL aerosol characterization instruments are field deployable, allowing researchers to capture aerosol data on location, in real time. Other instruments are used for comprehensive off-line characterization of atmospheric aerosols.


EMSL hosts a number of unique mass spectrometry instruments specially configured for studying fundamental aspects of activation, dissociation, and deposition (soft-landing) of complex molecular ions following collision with specially prepared surfaces. EMSL researchers use a combination of experimental studies of collisional activation and dissociation of complex molecules in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer with RRKM modeling to determine the internal energy distribution of excited ions and the energetics and dynamics of dissociation of a variety of complex ions and non-covalent complexes. Preparatory mass spectrometry using soft-landing of mass selected ions on surfaces enables highly specific modification of surfaces, preparation of novel materials, and facilitates molecular level understanding of interactions of biomolecules with hydrophilic and hydrophobic surfaces in living systems.

Capability Detail

Refer to the table below for a full listing, which leads to complete information about each of EMSL's mass spectrometry instruments. Brief details about the primary mass spectrometry tools available to EMSL users immediately follow.

Proteomics Capabilities

Aerosol and Ion-Surface Collision Capabilities

  1. Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium.
  2. Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch.
  3. Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens.
  4. A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum.
  5. Resin-assisted enrichment of thios as a general strategy for proteomic profiling of cysteine-based reversible modifications.
  1. Study reveals new insights into sulfate-reducing bacteria (Bioenergetic pathways)
  2. Iron-bearing minerals in sediments naturally reduce contaminant levels (Lack of iron)
  3. Redox cycling by DsrC protein suggests reason for interaction with dissimilatory sulfite reductase (Step at a time)
  4. SCF1 frees plant sugars in lignin for sustainable biofuels (Biofuel breakdown)
  5. Soil pretreatment boosts protein recovery for microbial community studies (Ditch the dirt)

Mass Spectrometry Capabilities Available at EMSL

Instrument Contact
Laser Ablation Sampling System Alexander, M Lizabeth
Mass Spectrometer: Fourier-Transform Ion Cyclotron Resonance Tolic, Ljiljana Pasa
Mass Spectrometer: FT-ICR, 6T (Ion Surface Collisions) Laskin, Julia
Mass Spectrometer: Inductively Coupled Plasma (ICP-MS) System, Metallomics Koppenaal, David
Mass Spectrometer: LC Triple Quadrupole Robinson, Robby
Mass Spectrometer: Linear Ion trap (LTQ) Moore, Ron
Tolic, Ljiljana Pasa
Mass Spectrometer: Orbitrap Moore, Ron
Tolic, Ljiljana Pasa
Mass Spectrometer: Aerosol, time-of-flight, high resolution Alexander, M Lizabeth
Mass Spectrometer: GC MS Tolic, Ljiljana Pasa
Mass Spectrometer: Inductively Coupled Plasma (ICP-MS) Wietsma, Tom
Mass Spectrometer: Inductively Coupled Plasma (ICP-MS), High Resolution (Element XR) Alexander, M Lizabeth
Mass Spectrometer: Inductively Coupled Plasma (ICP-MS), Multi-Collector (Neptune Plus) Alexander, M Lizabeth
Mass Spectrometer: Inductively Coupled Plasma (ICP-MS), Ultra-High Resolution Koppenaal, David
Mass Spectrometer: Ion Mobility Spectrometry, Time of Flight Robinson, Robby
Mass Spectrometer: Linear Ion Trap Quadrupole (LTQ) Orbitrap MS - for environmental research (nanoDESI) Laskin, Alexander
Mass Spectrometer: MALDI-TOF Chu,Rosalie K
Robinson, Robby
Mass Spectrometer: Proton Transfer Reaction (PTRMS) Alexander, M Lizabeth
Mass Spectrometer: Single Particle (SPLAT II) Zelenyuk, Alla
Mass Spectrometer: Time of Flight Secondary Ion (ToF SIMS) - 1997 Laskin, Julia
Mass Spectrometer: Time of Flight Secondary Ion (ToF SIMS) - 2007 Zhu, Zihua
Mass-Selected Ion Deposition System - Electrospray Source Laskin, Julia
Spectrometer: High Spatial Resolution Secondary Ion Mass Spectrometry (NanoSIMS) Zhu, Zihua
Mass Spectrometry Capability Lead Interim (Proteomics): Robby Robbinson | , 509-371-6341
Mass Spectrometry Capability Lead (Materials): Theva Thevuthasan | , 509-371-6244