Lab Capabilities

The Mass Spectrometry lab (MSL) and the Analytical Proteomics Lab (APL) operate and maintain a suite of high performance mass spectrometers with most coupled to high resolution separation devices.  The mass analyzers support a variety of ionization techniques; matrix assisted laser desorption (MALDI), electrospray and atmospheric chemical (ESI and APCI), fast atom bombardment (FAB) and the classic electron and chemical (EI and CI). 


The lab has a capillary gas chromatograph as an inlet to a triple quadrupole mass spectrometer that supports EI and CI ionization, commonly abbreviated GC/MS.  For separation in the liquid phase, the lab has micro-capillary, nano-high pressure and ultra-high pressure liquid chromatographs enabling the lab to run HPLC or UPLC/MS or HPLC MS/MS experiments. The liquid chromatographs (located in Malott Hall) are arranged in an instrument room such that the Waters Qtof Premier (Qtof) or Quattro ultima “triple” quadrupole (QQQ) can be interfaced to micro, capillary or ultra-pressure LC by choosing the Water 2695, CapLC or acquity classic UPLC. The staff can assist in choosing the appropriate combination for HPLC/MS or HPLC/MS/MS experiments.

Bio-Molecule Projects

The more demanding, high sensitivity, protein characterization or other bio-molecule projects are conducted in the APL on the Thermo LTQFT linear ion trap-ion cyclotron resonance hybrid instrument or the Waters Synapt G2 quadrupole time of flight instrument with ion mobility, QTOF/IMS. Both instruments have nano-UPLC separation devices, Waters nanoAcquity, for separations on nano or capillary columns (typically 75 or 300u id columns operated at 0.8 or 12 ul/min flow rates).  Experiments on these high resolution instruments normally utilize tandem MS features for additional structural information by fragmentation (ms/ms or mse) via collision induced dissociation (CID).

MALDI and FAB ionization are older instruments and are used in manual mode where samples plus matrix are applied on plate or stage and introduced by a staff operator.

Data Acquisition

The lab workstations that can be used to interrogate mass spectrometric data on the instruments “native” data system are the Xcalibur, MassLynx or ABI Data Explorer.  Charge state diversity to “single” charge spectra is done with a tansform routine or one of the MaxEnt routines in Masslynx.  Post acquisition software packages are available for specialized experiments.  The most extensive are the proteomics data processing in the APL. In addition there is software for quantitation with Quanlynx, protein mapping with BioPharmalynx and biomarker discovery using MarkerLynx.



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