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 effect of anthropogenic and biogenic organic particles on atmospheric glaciation processes is poorly understood. We use an optical microscopy (OM...
Sources, optical properties, and chemical composition of atmospheric brown carbon (BrC) aerosol are uncertain, making it challenging to estimate its...
Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to...
Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (...
Due to their high sensitivity and specificity, targeted proteomics measurements, e.g. selected reaction monitoring (SRM), are becoming increasingly...

Science Highlights

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...
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...

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:

Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma

Abstract: 

Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 µL) due to low yields stemming from losses caused by nonspecific binding to the column matrix. Additionally, the cost of the depletion media can be prohibitive for larger scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large scale studies. We characterized the performance of a 346 µL column volume micro-scale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6 μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10 mL depletion column served as the control. Results showed depletion efficiency of the micro-scale column increased as flow rate decreased, and that our micro-depletion was reproducible. In an initial application, a 600 µL sample of human cerebral spinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.  

Citation: 
Hyung SW, PD Piehowski, RJ Moore, DJ Orton, AA Schepmoes, TRW Clauss, RK Chu, TL Fillmore, HM Brewer, T Liu, R Zhao, and RD Smith.2014."Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid."Analytical and Bioanalytical Chemistry 406(28):7117-7125. doi:10.1007/s00216-014-8058-3
Authors: 
SW Hyung
PD Piehowski
RJ Moore
DJ Orton
AA Schepmoes
TRW Clauss
RK Chu
TL Fillmore
HM Brewer
T Liu
R Zhao
RD Smith
Facility: 
Instruments: 
Volume: 
406
Issue: 
28
Pages: 
7117-7125
Publication year: 
2014

Effect of Solar Radiation on the Optical Properties and Molecular Composition of Laboratory Proxies of Atmospheric Brown Carbon

Abstract: 

Sources, optical properties, and chemical composition of atmospheric brown carbon (BrC) aerosol are uncertain, making it challenging to estimate its contribution to radiative forcing. Furthermore, optical properties of BrC may change significantly during its atmospheric aging. We examined the effect of solar photolysis on the molecular composition, mass absorption coefficient, and fluorescence of secondary organic aerosol prepared by high-NOx photooxidation of naphthalene (NAP SOA). The aqueous solutions of NAP SOA was observed to photobleach with an effective half-time of 15 hours (with sun in its zenith) for the loss of the near-UV (300 -400 nm) absorbance. The molecular composition of NAP SOA was significantly modified by photolysis, with the average SOA formula changing from C14.1H14.5O5.1N0.08 to C11.8H14.9O4.5N0.02 after 4 hours of irradiation. The average O/C ratio did not change significantly, however, suggesting that it is not a good metric for assessing the extent of photolysis-driven aging in NAP SOA (and in BrC in general). In contrast to NAP SOA, the photolysis of BrC material produced by aqueous reaction of limonene+O3 SOA (LIM/O3 SOA) with ammonium sulfate was much faster, but it did not result in a significant change in the molecular level composition. The characteristic absorbance of the aged LIM/O3 SOA in the 450-600 nm range decayed with an effective half-time of <0.5 hour. This result emphasizes the highly variable and dynamic nature of different types of atmospheric BrC.

Citation: 
Lee HJ, PK Aiona, A Laskin, J Laskin, and S Nizkorodov.2014."Effect of Solar Radiation on the Optical Properties and Molecular Composition of Laboratory Proxies of Atmospheric Brown Carbon ."Environmental Science & Technology 48(17):10217-10226. doi:10.1021/es502515r
Authors: 
HJ Lee
PK Aiona
A Laskin
J Laskin
S Nizkorodov
Volume: 
48
Issue: 
17
Pages: 
10217-10226
Publication year: 
2014

Micro-Spectroscopic Imaging and Characterization of Individually Identified Ice Nucleating Particles from a Case Field Study.

Abstract: 

The effect of anthropogenic and biogenic organic particles on atmospheric glaciation processes is poorly understood. We use an optical microscopy (OM) setup to identify the location of ice nuclei (IN) active in immersion freezing and deposition ice nucleation for temperatures of 200-273 K within a large population of particles sampled from an ambient environment. Applying multi-modal micro-spectroscopy methods we characterize the physicochemical properties of individual IN in particle populations collected in central California. Chemical composition and mixing state analysis of particle populations are performed to identify characteristic particle-type classes. All particle-types contained organic material. Particles in these samples take up water at subsaturated conditions, induce immersion freezing at subsaturated and saturated conditions above 226 K, and act as deposition IN below 226 K. The identified IN belong to the most common particle-type classes observed in the field samples: organic coated sea salt, Na-rich, and secondary and refractory carbonaceous particles. Based on these observations, we suggest that the IN are not always particles with unique chemical composition and exceptional ice nucleation propensity; rather, they are common particles in the ambient particle population. Thus, particle composition and morphology alone are insufficient to assess their potential to act as IN. The results suggest that particle-type abundance is also a crucial factor in determining the ice nucleation efficiency of specific IN types. These findings emphasize that ubiquitous organic particles can induce ice nucleation under atmospherically relevant conditions and that they may play an important role in atmospheric glaciation processes.

Citation: 
Knopf DA, PA Alpert, B Wang, RE O'Brien, ST Kelly, A Laskin, MK Gilles, and RC Moffet.2014."Micro-Spectroscopic Imaging and Characterization of Individually Identified Ice Nucleating Particles from a Case Field Study."Journal of Geophysical Research. D. (Atmospheres) 119(17):10,365-10,381. doi:10.1002/2014JD021866
Authors: 
DA Knopf
PA Alpert
B Wang
RE O'Brien
ST Kelly
A Laskin
MK Gilles
RC Moffet
Facility: 
Instruments: 
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Molecular Selectivity of Brown Carbon Chromophores.

Abstract: 

Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

Citation: 
Laskin J, A Laskin, S Nizkorodov, PJ Roach, PA Eckert, MK Gilles, B Wang, HJ Lee, and Q Hu.2014."Molecular Selectivity of Brown Carbon Chromophores."Environmental Science & Technology 48(20):12047-12055. doi:10.1021/es503432r
Authors: 
J Laskin
A Laskin
S Nizkorodov
PJ Roach
PA Eckert
MK Gilles
B Wang
HJ Lee
Q Hu
Volume: 
48
Issue: 
20
Pages: 
12047-12055
Publication year: 
2014

Expediting SRM assay development for large-scale targeted proteomics experiments.

Abstract: 

Due to their high sensitivity and specificity, targeted proteomics measurements, e.g. selected reaction monitoring (SRM), are becoming increasingly popular for biological and translational applications. Selection of optimal transitions and optimization of collision energy (CE) are important assay development steps for achieving sensitive detection and accurate quantification; however, these steps can be labor-intensive, especially for large-scale applications. Herein, we explored several options for accelerating SRM assay development evaluated in the context of a relatively large set of 215 synthetic peptide targets. We first showed that HCD fragmentation is very similar to CID in triple quadrupole (QQQ) instrumentation, and by selection of top six y fragment ions from HCD spectra, >86% of top transitions optimized from direct infusion on QQQ instrument are covered. We also demonstrated that the CE calculated by existing prediction tools was less accurate for +3 precursors, and a significant increase in intensity for transitions could be obtained using a new CE prediction equation constructed from the present experimental data. Overall, our study illustrates the feasibility of expediting the development of larger numbers of high-sensitivity SRM assays through automation of transitions selection and accurate prediction of optimal CE to improve both SRM throughput and measurement quality.

Citation: 
Wu C, T Shi, JN Brown, J He, Y Gao, TL Fillmore, AK Shukla, RJ Moore, DG Camp, II, KD Rodland, W Qian, T Liu, and RD Smith.2014."Expediting SRM assay development for large-scale targeted proteomics experiments."Journal of Proteome Research 13(10):4479-87. doi:10.1021/pr500500d
Authors: 
Wu C
T Shi
JN Brown
J He
Y Gao
TL Fillmore
AK Shukla
RJ Moore
DG Camp
II
KD Rodl
W Qian
T Liu
RD Smith
Capabilities: 
Volume: 
13
Issue: 
10
Pages: 
4479-87
Publication year: 
2014

Carbon Mineralizability Determines Interactive Effects onMineralization of Pyrogenic Organic Matter and Soil Organic Carbon.

Abstract: 

Soil organic carbon (SOC) is a critical and active pool in the global C cycle, and the addition of pyrogenic organic matter (PyOM) has been shown to change SOC cycling, increasing or decreasing mineralization rates (often referred to as priming). We adjusted the amount of easily mineralizable C in the soil, through 1-day and 6-month pre-incubations, and in PyOM made from maple wood at 350°C, through extraction. We investigated the impact of these adjustments on C mineralization interactions, excluding pH and nutrient effects and minimizing physical effects. We found short-term increases (+20-30%) in SOC mineralization with PyOM additions in the soil pre-incubated for 6 months. Over the longer term, both the 6-month and 1-day pre-incubated soils experienced net ~10% decreases in SOC mineralization with PyOM additions. This was possibly due to stabilization of SOC on PyOM surfaces, suggested by nanoscale secondary ion mass spectrometry. Additionally, the duration of pre-incubation affected priming interactions, indicating that there may be no optimal pre-incubation time for SOC mineralization studies. We show conclusively that relative mineralizability of SOC in relation to PyOM-24 C is an important determinant of the effect of PyOM additions on SOC mineralization.

Citation: 
Whitman TL, Z Zhu, and JC Lehmann.2014."Carbon Mineralizability Determines Interactive Effects onMineralization of Pyrogenic Organic Matter and Soil Organic Carbon."Environmental Science & Technology 48(23):13727-13734. doi:10.1021/es503331y
Authors: 
TL Whitman
Z Zhu
JC Lehmann
Instruments: 
Volume: 
48
Issue: 
23
Pages: 
13727-13734
Publication year: 
2014

Improved protocol to purify untagged amelogenin - Application to murine amelogenin containing the equivalent P70 → T point

Abstract: 

Amelogenin is the predominant extracellular protein responsible for converting carbonated hydroxyapatite into dental enamel, the hardest and most heavily mineralized tissue in vertebrates. Despite much effort, the precise mechanism by which amelogenin regulates enamel formation is not fully understood. To assist efforts aimed at understanding the biochemical mechanism of enamel formation, more facile protocols to purify recombinantly expressed amelogenin, ideally without any tag to assist affinity purification, are advantageous. Here we describe an improved method to purify milligram quantities of amelogenin that exploits its high solubility in 2% glacial acetic acid under conditions of low ionic strength. The method involves heating the frozen cell pellet for two 15 min periods at ~70 ºC with two minutes of sonication in between, dialysis twice in 2% acetic acid (1:250 v/v), and reverse phase chromatography. A further improvement in yield is obtained by resuspending the frozen cell pellet in 6 M guanidine hydrochloride in the first step. The acetic acid heating method is illustrated with a murine amelogenin containing the corresponding P70T point mutation observed in an human amelogenin associated with amelogenesis imperfecta (P71T), while the guanidine hydrochloride heating method is illustrated with wild type murine amelogenin (M180). The self-assembly properties of P71T were probed by NMR chemical shift perturbation studies as a function of protein (0.1 to 1.8 mM) and NaCl (0 to 367 mM) concentration. Relative to similar studies with wild type murine amelogenin, P71T self-associates at lower protein or salt concentrations with the interactions initiated near the N-terminus.

Citation: 
Buchko GW, and WJ Shaw.2015."Improved protocol to purify untagged amelogenin - Application to murine amelogenin containing the equivalent P70 ? T point mutation observed in human amelogenesis imperfecta."Protein Expression and Purification 105(1):14-22. doi:10.1016/j.pep.2014.09.020
Authors: 
GW Buchko
WJ Shaw
Instruments: 
Volume: 
105
Issue: 
1
Pages: 
14-22
Publication year: 
2015

Molecular Characterization of Organic Content of Soot along the Centerline of a Coflow Diffusion Flame.

Abstract: 

High-resolution mass spectrometry coupled with nanospray desorption electrospray ionization was used to probe chemical constituents of young soot particles sampled along the centerline of a coflow diffusion flame of a three-component Jet-A1 surrogate. In lower positions where particles are transparent to light extinction (n= 632.8 nm), peri-condensed polycyclic aromatic hydrocarbons (PAHs) are found to be the major components of the particle material. These particles become enriched with aliphatic components as they grow in mass and size. Before carbonization occurs, the constituent species in young soot particles are aliphatic and aromatic compounds 200-600 amu in mass, some of which are oxygenated. Particles dominated by PAHs or mixtures of PAHs and aliphatics can both exhibit liquid-like appearance observed by electron microscopy and be transparent to visible light. The variations in chemical composition observed here indicate that the molecular processes of soot formation in coflow diffusion flames may be more complex than previously thought. For example, the mass growth and enrichment of aliphatic components in an initially, mostly aromatic structure region of the flame that is absent of H atoms or other free radicals indicates that there must exist at least another mechanism of soot mass growth in addition to the hydrogen-abstraction-carbon addition mechanism currently considered in fundamental models of soot formation.

Citation: 
Cain JP, A Laskin, MR Kholghy, M Thomson, and H Wang.2014."Molecular Characterization of Organic Content of Soot along the Centerline of a Coflow Diffusion Flame."Physical Chemistry Chemical Physics. PCCP 16(47):25862 - 25875. doi:10.1039/c4cp03330b
Authors: 
JP Cain
A Laskin
MR Kholghy
M Thomson
H Wang
Facility: 
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

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