Mass Specs at UVM

Mass Spectrometry at the University of Vermont

In Prof. Matthews' Laboratory, Dept. of Chemistry, Cook Physical Sciences Building

Thermo-Finnigan LTQ Linear Quadrupole Ion Trap Mass Spectrometer Plus Liquid Chromatograph (LCMS)

  • Installed February 2006
  • Mass separation by a linear quadrupole ion trap; m/z = 50-2000 mass range
  • Electrospray ionization (ESI) and nanospray-ESI interfaces for liquid sample introduction
  • Shimadzu Prominence HPLC system with autosampler and two pumps
  • Controlled by the Finnigan XCALIBUR data system on a PC
  • Shown in photo: our home-made nanospray stage and microcapillary HPLC column
Finnigan LTQ LCMS
  • The linear ion trap can perform MSn collision induced dissociation (CID) experiments
  • The system can be set (i) for 1D HPLC separation of peptides using a micro-C18 column and micro-ESI and (ii) for MudPIT 2D HPLC analysis of complex peptide mixtures using a capillary packed with strong cation exchange and C18 that forms the tip of the nano-ESI. In 1D mode, peptides are injected through the autosampler onto the micro C18 column. In 2D mode, samples are pre-loaded onto the 2D nanocolumn and eluted using the autosampler to provide the "salt bumps" of increasing salt concentration.
  • The system processes peptide data (i) under Thermo-Finnigan SEQUEST as part of the Bioworks package and (ii) under DTA-Select (©The Scripps Research Institute)

Thermo-Finnigan LCQ Deca XP Ion Trap Mass Spectrometer Plus Liquid Chromatograph (LCMS)

  • Mass separation by a quadrupole ion trap; m/z = 50-2000 or 100-4000 mass ranges
  • ESI and nanospray-ESI interfaces for liquid sample introduction (nanospray is shown in the photo)
  • Thermo-Finnigan Surveyor HPLC system with autosampler and with two quarternary pumps for 2D-LC
  • Controlled by the Finnigan XCALIBUR data system on a PC
Finnigan LCQ Deca XP Plus
  • The ion trap can perform MSn CID experiments
  • The system is set up for both 1D and 2D HPLC separations. In the 2D mode, peptides are injected through the autosampler onto a micro ion exchange column. Groups of peptides are washed from the ion exchange onto one of two fused-silica capillaries packed with C18 phase when increasing steps of salt are applied to the ion exchange column. The C18-packed capillaries are attached to a 10-port valve so that one column will receive peptides from the ion exchange column while peptides from the prior wash are being eluted from the other C18 column into the LCQ.
  • The system processes peptide data (i) under Thermo-Finnigan SEQUEST as part of the Bioworks package and (ii) under DTA-Select (©The Scripps Research Institute)

Thermo-Finnigan TSQ 700 liquid chromatograph-mass spectrometer (LCMS) upgraded from a 70

  • Operates with both ESI and atmospheric pressure chemical ionization (APCI) interfaces for liquid sample introduction
  • The 1st and 3rd quadrupole rod sets can be set for either a m/z = 0-2000 or 4000 mass ranges
  • The middle quadrupole rods function in radio frequency-only mode as the CID chamber for performing tandem (MS/MS) experiments
Finnigan TSQs
  • The instruments are controlled by a Finnigan ICIS data system operating under UNIX on a DEC Alpha workstations
  • On the left: Waters 2695 HPLC system with a model 717 96-vial autosampler, quaternary solvent system and Millennium32 software system on a separate PC.  The HPLC can be controlled through the front panel or through the Millennium software and can be interfaced to either the TSQ or the LCQ Deca XP.

Thermo-Finnigan MAT DeltaPlus Gas Chromatograph - Combustion - Isotope Ratio Mass Spectrometer (GC-C-IRMS)

  • Mass separation by electromagnet; m/z = 0-70 mass range at 3 kV
  • Triple Faraday-cup collector system for measuring the isotopes of 13C, 18O, or 15N from CO2 or N2 gases
  • Samples injected into the HP6890 GC (with CTC A200S autosampler) then into the Finnigan GCC-III combustion/reduction interface (oxidation oven at 960 °C shown on top of GC)
  • Controlled by Finnigan Isodat data system on a PC
Finnigan Delta
  • Purpose: to measure 13C and 15N isotope ratios from organic compounds eluting from the GC.
  • Precision in the GC continuous-flow mode: <0.5 ‰ for 13C and 15N for <1 and 2 nmol of CO2 and N2 respectively.

In Biochemistry, in the Given Building

Applied Biosystems Voyager-DE Pro Biospectrometry Workstation Matrix-Assisted Laser Desorption-Time of Flight (MALDI-TOF) Mass Spectrometer

  • With a 337-nm N2 3-ns pulse UV laser and delayed extraction after photoionization
MALDI-TOF Under the hood of the MALDI-TOF
Any photo of the MALDI-TOF looks like a boring box (even after including Mark Jennings as the operator)
  The above is an "under the hood" photo the Applied Biosystems MALDI-TOF DE-Pro with the cover off.
  • 1.3-m linear flight tube with a ~300-kDa mass range and a resolution of >2000 for small proteins (m/z <20 kDa) and ~50 for large proteins (m/z ~100 kDa)
  • 2.0-m flight tube in “reflectron” mode with resolution of >7,000 at m/z <6 kDa
  • Positive and negative ion measurement
  • “Post-source decay” capability

In the General Clinical Research Center (GCRC) Core Laboratory in the Cook Physical Sciences Building

Europa Hydra 20/20 Gas Chromatograph - Pyrolysis - Isotope Ratio Mass Spectrometer (GC-P-IRMS)

  • With a HP6890 GC and HP7683 autosampler attached (on the left)
  • Electromagnet analyzer; mass range is m/z = 1-70 at 3 kV
Europa 20/20 Hydra
  • Triple Faraday collector system for measuring the isotopes of 13C, 18O, or 15N from CO2, CO, or N2 gases
  • With a Hydra flight tube equipped with a special spur to collect m/z=3 of H2 for 2H measurement in a Faraday cup, while collecting m/z=2 in the regular Faraday cup array. This scheme allows large separation of m/z = 2 & 3 and large separation of m/z = 3 from 4 (from the He carrier gas).
  • Two different pyrolysis interfaces between the GC and IRMS to provide sensitive measurement of 2H and 18O:
    • One to reduce injected water or urine samples to H2 and CO
    • Another to convert organic compounds eluting from the GC to H2 and CO
  • An ABCA-G gas inlet system (not shown to the right) with auto-injector is also installed to process H2 or CO2 gas samples from Exatainer tubes for measurement of 2H, 13C or 18O

Hewlett Packard HP-5973 Gas Chromatograph - Mass Spectrometer (GCMS)

  • HP6890 GC with an HP7683 autosampler
  • Quadrupole mass analyzer; m/z = 0-800 mass range
  • Electron impact (EI) ionization
  • Negative (NCI) and positive chemical ionization (PCI)
  • Used for measuring stable isotopic enrichments in metabolites of biological samples in the range of 0.5 -10 mole % excess (mpe) tracer by selected ion monitoring (SIM).
HP5973 GCMS

Hewlett Packard HP-5971 GCMS

  • HP5890 GC with an HP7673B autosampler
  • Quadrupole mass analyzer; m/z = 0-650 mass range
  • Electron impact (EI) ionization
  • Used for measuring stable isotopic enrichments in metabolites of biological samples by SIM
HP5971 GCMS

Also in the Dept. of Chemistry, Cook Physical Science Building

Finnigan 4000 GCMS

  • Quadrupole mass filter; m/z = 10-2000 mass range
  • Operated under electron ionization (EI)
  • Direct insertion probe for sample introduction

Hewlett Packard 5988A GCMS

  • With HP5890A GC and HP7673A autosampler
  • Quadrupole mass filter; m/z = 10-1000 mass range
  • Operates in EI, positive chemical ionization (PCI) or negative chemical ionization (NCI) modes