Instruments and Capabilities

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The 7T LTQ FT Ultra mass spectrometer (an FT-ICR mass spectrometer).


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The LTQ XL mass spectrometer (a linear ion trap mass spectrometer).


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The TSQ Vantage mass spectrometer (a triple quadrupole mass spectrometer).


FT-ICR Mass Spectrometer (FT-ICR MS)


The cornerstone of the facility is a 7 T Fourier-transform ion cyclotron resonance mass spectrometer
(FT-ICR MS) from Thermo Scientific (LTQ FT Ultra hybrid mass spectrometer). The front-end of the instrument is a linear ion trap mass spectrometer (LTQ MS) which serves as the ion accumulation site for ultra high resolution analysis in the ICR cell. The mass range for the instrument is 50-2000 m/z; though in practice, only a portion of this mass range is analyzed at any one time. The FT-ICR MS provides ultra high resolution and high mass accuracy for ions within complex samples, i.e., <1 ppm mass accuracy or + 0.0001 Da at 400 Da. A liquid chromatography interface, UV-Vis detector, versatile atmospheric ionization sources, and multiple MS fragmentation options (see below) provide optimum flexibility in the characterization of a broad range of environmental samples.

LTQ Mass Spectrometer (LTQ MS)


A stand-alone linear ion trap mass spectrometer (Thermo LTQ XL) is available for method development, sample screening, and for applications that do not require ultra high mass resolution. The LTQ MS is identical to the front end of the FT-ICR MS and methods developed on the LTQ MS are fully transferable to the FT-ICR MS. All ionization sources and software applications described below can be used with the LTQ mass spectrometer. Structural characterization of compounds is possible through MSn fragmentation capabilities (collision induced dissociation). Quantitative analysis via LC-MS is also possible.


Triple Quadrupole Mass Spectrometer (TSQ MS)


A triple quadrupole mass spectrometer (Thermo TSQ Vantage) is available for targeted and quantitative analyses of a wide variety of small molecules (hormones, metabolites, environmental contaminants, peptides, etc.). The TSQ Vantage is couple to a HPLC/UPLC system (Thermo Accela pump with open autosampler) for fast and highly sensitive analyses of compounds in complex matrices.

Ionization Sources


Five different ionization sources are available for use with the mass spectrometers:
 
1-2) micro- and nano-electrospray ionization (ESI)
3) atmospheric pressure chemical ionization (APCI)

4) matrix-assisted laser desorption ionization (MALDI)
5) atmospheric pressure photo ionization (APPI) NEW

The micro-ESI source is used for direct infusion of sample and for introduction of HPLC effluent. Nano-ESI is ideal for small sample quantities and low-flow HPLC effluents. These low flow rates have been shown to enhance separation in complex mixtures and reduce solvent introduction into the mass spectrometer. The nano-ESI probe has two components - a static nano-spray probe for small samples with no HPLC pre-separation and a dynamic nano-spray probe for samples that require HPLC pre-separation. Both the micro-ESI and nano-ESI sources can be used to examine polar macromolecules, such as specific components of organic matter or protein samples. The APCI source can be used for those studies that require analysis of semi-volatile compounds such as petroleum products. The atmospheric-pressure MALDI source can be used for analysis of large non-volatile macromolecules.

NanoMate Ionization Source


An additional ionization system is available for analysis on the FT-ICR MS.  The TriVersa NanoMate™ from Advion
Biosystems, Inc. acts as both a nanospray ionization source and a fraction collector. Samples can be introduced into the mass spectrometer directly from a 96-well plate in the NanoMate. Alternatively, samples can be separated with liquid chromatography and the effluent is split between the ionization source and the fraction collector. This allows repeat analysis of chromatographic fractions by direct nanospray infusion into the FT-ICR MS.


Fragmentation Options


For projects requiring structural characterization of selected molecules,
the FT-ICR MS is equipped with three different fragmentation methods:

1) Fragmentation by collision-induced dissociation (CID) in the linear ion trap followed by FT-ICR MS analysis. This fragmentation option is most suitable for users with prior MS/MS data acquisition on a lower-resolution mass spectrometer and provides ultrahigh mass resolution for CID fragments.

2) E
lectron capture dissociation (ECD) within the ICR cell for fragmentation of multiply-charged ions. ECD is particularly appropriate for fragmentation of proteins, which often carry up to 15 charges per ion. ECD preferentially breaks the protein along the peptide backbone, preserving the type and location of post-translational modifications. The protein sequence is then deduced from the fragmentation pattern, providing “top-down” sequence information.
 
3) Infrared multiphoton dissociation (IRMPD) can be used to fragment ions within the ICR cell regardless of charge state. IRMPD provides a nice complement to CID fragmentation spectra due to the lack of a lower-mass cutoff for IRMPD fragments. If necessary, both ECD and IRMPD can be applied to the same compound due to the placement of the CO2 laser (IRMPD) within the hollow cathode of the ECD.



Data Analysis

Software for generating elemental formulas for natural organic matter samples has been developed by E. Kujawinski and is available for data analysis of samples run at the Facility.

BioWorks™ is a program that enables efficient searching of protein databases. This is used primarily for enzymatic digests of proteins or protein extracts but can be used for intact protein spectra as well. Mass Frontier™ predicts fragmentation spectra for proposed compound structures. A stand-alone workstation is available to users for analysis of data collected in the facility using any of the software describe above.

We have also significantly expanded our data storage capacity with a 12 TB, RAID 5 Snap Server, and will temporily store user data for up to one year.



 

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Last updated March 23, 2011
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