Equipment

The Thermo Scientific Orbitrap Elite MS is a high-performance hybrid mass spectrometer combining the novel high-field Orbitrap analyzer with a dual-pressure linear ion trap. It features advanced mass spectrometry/mass spectrometry functions, atmospheric pressure ionization (electrospray ionization, atmospheric pressure chemical ionization, and atmospheric pressure photoionization), and quantitation and spectral consistency range to the femtogram level, allowing identification and quantification of a wide range of compounds in studies of environmental chemistry, biochemistry, metabolomics, biomarkers, organic pollutants, and more.

Instrument Performance

• Very high resolving power—up to 240,000 FWHM—facilitates analysis of low-abundance components in complex samples and resolves isobaric species and isotope fine structures with confidence
• Ion optics with novel neutral-blocking technology and an advanced detection system increase system robustness and quantification capabilities
• Advanced signal processing combined with fast scanning ensures UHPLC compatibility
• Multiple fragmentation techniques—CID, HCD, and optionally ETD—provide versatility and complementary data
• Innovative pre-amplifier electronics improve sensitivity
• Parallel MS and MSn capability speeds analyses

Small Molecule Omics-Inspired Research Capabilities

• Very high resolution distinguishes components in complex matrices
• Sensitivity ensures detection of more analytes
• High-quality MSn spectral trees provide extensive structural information for metabolite identification and the location of modification sites
• Improved robustness lowers maintenance, enabling 24/7 operation when running complex biological matrices

Large Molecule Research Capabilities

• Very high resolution and complementary fragmentation modes facilitate top-down protein identification and characterization
• ETD option preserves labile side chains while fragmenting the peptide backbone for improved analysis of PTMs
• Fast scanning combined with high resolution and high spectral quality yields more protein identifications in a single analysis
• Very high resolution and selectivity in both full-scan MS and MSn modes enhance relative quantification results from stable isotope labeling or isobaric mass tagging experiments

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The Thermo Scientific LCQ Fleet MS system provides cost-effective, high quality, structural information for routine analysis of complex samples on a high-throughput basis. It integrates seamlessly with fast HPLC systems under a convenient single point of control. Equipped with many advanced features, including MSn, a powerful tool for confident structural characterization, the LCQ Fleet enables all users, from novice to expert, to easily analyze and interpret sample data.

Performance Highlights

• Unique, proprietary Automatic Gain Control (AGC) ensures that the ion trap is always filled with the optimum number of ions for any scan type
• Dynamic Exclusion allows acquisition of MS/MS and MSn spectra from lower intensity ion species
• WideBand Activation generates more structurally informative spectra
• Normalized Collision Energy compensates for the mass-dependent energy deposition characteristics, providing reproducible data from instrument to instrument
• Pulsed-Q Dissociation (PQD) enables trapping of low-mass fragment ions
• Charge state determinations up to three with ZoomScan
• Data-Dependent Acquisition enables automated analysis of unknowns

Scan Functions

• Full-scan feature provides full-scan mass spectra for sensitive analyses and produces spectra for rapid screening of unknown compounds
• Selected Ion Monitoring (SIM) monitors selected ions for target compound analysis
• Full-scan MS/MS produces fast, full scan, information rich, product ion spectra
• Selected Reaction Monitoring (SRM) for a traditional LC/MS/MS quantitative analytical experiment MSn for multi-stage MS experiments to probe the structure of ions
• ZoomScan a high-resolution, full-range scan to resolve isotopic envelopes, which is often used for charge state determination of peptides and oxidation state determination of organometallics
• TurboScan an ultra-fast scan to improve signal-to-noise and sampling rate 

The Thermo Scientific ITQ 1100 gas chromatograph/mass spectrometer, features advanced mass spectrometry/mass spectrometry functions, pulsed positive ion negative ion/chemical ionization, and quantitation and spectral consistency range to the femtogram level, allowing identification and quantification of a wide range of compounds in studies of biochemistry, metabolomics, eco-toxicity, biomarkers in the geosphere and ambient environment, organic pollutants, and many others.

Instrument Features and Tools

• NIST Mass Spectral Library
• Unit mass resolution throughout the mass range 10 to 1100 amu in full-scan mode
• Both positive and negative chemical ionization modes supported; digital reagent gas flow control ensures method stability and reproducibility
• MSn with ACE and PQD
• Automated Collision Energy (ACE) automatically calculates an estimated optimal collision energy based on product ion m/z and damping gas flow rates; runs at three energies across each scan
• Pulsed Q Dissociation Mode (PQD) generates information-rich mass spectral data, even in the low mass range; produces precise, reproducible fragmentation
• Restore system performance, change from EI to Cl, or use the direct sample probe without venting the instrument using the Vacuum Probe Interlock
• Independently controlled heating from 125° to 300°C for stable operation and excellent chromatographic integrity
• Automatic gain control ensures that the ion trap is always filled with the optimum number of ions
• Post-acceleration +10kV conversion dynode offers efficient positive and negative ion detection

Our Thermo Scientific ELEMENT 2 inductively coupled plasma/mass spectrometer is capable of rapidly measuring elemental and isotopic composition. The ELEMENT 2 is a high performance, double focusing magnetic sector field ICP-MS optimized for ease-of-use, stability, and productivity. The ELEMENT 2 provides access to a powerful technique to solve a specific problem, combined with excellent sensitivity and signal-to-noise ratio.

ICP-MS is the accepted and most powerful technique for the analysis and quantification of trace elements. Its applications range from the semiconductor industry to geological and environmental analyses, from biological research to material sciences. The most severe limitation of ICP-MS is polyatomic interference on the elemental signals, originating from Argon and/or the sample matrix. High Mass resolution is the gold standard for the identification and elimination of interference. Elimination of interference enables accurate and reliable quantitative multi-element analyses at trace levels, even without sample preparation.

Instrument Features and Tools

Multi-Elemental Analysis

• A multi-elemental detector with the speed to handle transient signals
• Interference-free measurement across the periodic table covering a mg/L to sub pg/L concentration range, from ultra-trace to matrix components
• Compatible with inorganic and organic solids and nearly all solution matrices

Full Automation for Routine Analysis

• Autotuning of all parameters, including lenses, gas flows, and the torch position for reproducible and reliable system setup
• Comprehensive, customizable, quality control system
• Reliability and robustness to serve as a 24/7 production control tool, maximizing sample throughput

Flexibility and Accessibility as an Advanced Research Tool

• Full access to all instrumental parameters for method development
• High mass resolution to access spectrally interfered isotopes: produces unambiguous elemental spectra
• High precision isotope ratios on non-interfered or interfered isotopes
• Hot and cold plasma conditions
• High stability for isotope ratios

The confocal/TIRF imaging system is based on Nikon optics, with three laser wavelengths selectable through an AOTF (488, 561, and 647). The spinning disk arm has a Yokogawa CSU-X1 spinning disc, confocal head with Borealis modification for flat illumination and more efficient light collection. The reflected light from SD Confocal is acquired by the ORCA-Flash sCMOS camera. The TIRF arm uses the three laser sources by manually switching the optical fiber of the laser to the TIRF illumination system. Reflected lights from the TIRF are also acquired by the same ORCA-Flash sCMOS camera, using manual brightfield bypass module for Yokogawa. The scope is fully enclosed in an Okolab stage-top incubation system with temperature and CO2 control designed for imaging mammalian cells. The system runs on Metamorph software.