Mass Spectrometry Facility Instrumentation

Last updated:
7/18/08

The MSF owns four mass spectrometers, two gas chromatographs, and one liquid chromatograph.  All of these instruments are located in Chemistry A411.  Brief descriptions of these instruments follow.  Click on any of the thumbnails for a 640x480 version of the image.  Rates quoted reflect FY2008 prices as of 8/14/07.  Note that if there is a significant change in the sample throughput, these rates can be altered.

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Agilent 1100 Capillary LC

(bought new (as demo equipment) in November 2004 with funds from Professors Peters, Oakley, DiMarchi, Stone, and the Chemistry Chairperson's Office)

The MSF's Agilent 1100 capillary liquid chromatograph may be used by itself or in tandem with either the API III or the MAT 95XP.  It has a thermostatted, 100-position autosampler compartment and has a variable wavelength (200-600 nm) UV-VIS absorbance detector with a 1 µL flow cell.  The pump can create reproducible gradients with flow rates from 1 to 2500 µL/min (assuming installation of the appropriate hardware), and can be coupled to the LCT or MAT-95 mass spectrometers or used by itself if mass information is not needed. 

Customers may use their own columns if they so desire, and the mass spectrometry facility has a handful of columns available.  Please be advised that for LC-MS applications, only volatile mobile phases and volatile mobile phase modifiers may be used.  We typically employ 0.3 mm i.d., 0.5 mm i.d., and 1 mm i.d. columns in our analyses.

Self-serve LC-MS with the LCT mass spectrometer costs $11.00/analysis, the cost is $25.00 if MSF staff perform LC-MS.

Please send any questions you may have concerning the 1100 CapLC to Jonathan Karty.  (Back to top)

Bruker Biflex III MALDI-TOF Mass Spectrometer

(bought new in March 2000 with funds from National Science Foundation grant 9970211)

The Bruker Biflex III is our matrix-assisted laser desorption/ionization (MALDI) reflectron time-of-flight mass spectrometer.  It is commonly used to analyze peptides, proteins, polymers, oligonucleotides and oligosaccharides.  If a customer's compound can absorb 337 nm light, this instrument can also be used for laser desorption/ionization (LDI) experiments.  Its capabilities in brief:

• Sources:  matrix-assisted laser desorption/ionization (MALDI), laser desorption/ionization (LDI)
• Inlets:  Off-line targets (384-well plate and a 12x10-position disk target holder)
• Mass analyzer:  reflectron time-of-flight
• Mass Range:  m/z 400-264,000 (linear, MALDI); m/z 400-5,800 (reflectron, MALDI); m/z 200-3,500 (reflectron, LDI)
• Mass accuracy:  (all assume quadratic curve fit with 4 calibrants):
  • Reflectron, external calibration:  ±60 ppm
  • Reflectron, internal calibration:  ±15 ppm
  • Linear, external calibration (m/z < 3000):  ±250 ppm
  • Linear, internal calibration (m/z < 3000):  ±60 ppm
  • Linear, external calibration (m/z > 3000):  ±1500 ppm
  • Linear, internal calibration (m/z > 3000):  ±300 ppm
• Resolution:
  • Reflectron:  10,000 @ m/z 3147
  • Linear:  4,000 @ m/z 1620

At present we request a minimum of 5 µL of a solution containing 10 µM analyte for peptide samples and 5 µL of a solution containing 50 µM analyte for protein samples.  Please remove all detergents (e.g. Triton X-100, SDS), chaotropes (e.g. urea, guanidinium HCl), and involatile liquids (e.g. glycerol) from sample prior to submission as these can prevent ionization and/or detection of your analyte.  Also, samples should have ionic strengths of 25 mM or less.  We recommend ZipTips™ for sample cleanup prior to MALDI MS.

Training is available for users who wish to record their own data with this instrument.  Please contact Jonathan Karty or Angela Hansen to set up an appointment.  Click here for some training materials.

Current rates for Chemistry Department users are $8.00/analysis for self-serve, $16 if MSF staff perform the analysis.

Please direct any questions concerning this instrument to Jonathan Karty or Angela Hansen.  (Back to top)

Agilent 6890N Gas Chromatograph and 5973 Inert Mass Selective Detector

(acquired new in June 2005 with funds from Professors Peters, Williams, Evans, the undergraduate teaching laboratories, and the Chemistry Department Chairperson's Office.  100-position autosampler tray purchased with MSF funds in July, 2006.

The Agilent 5973 Inert is a robust quadrupole mass spectrometer that can be fitted either with electron impact or chemical ionization sources.  It serves as the detector for the Agilent 6890N GC.  The 5973 Inert is the smaller box on the left-hand side of the photo.  Its capabilities in brief are:

• Sources:  electron ionization (EI); chemical ionization (CI, with CH₄, C₄H₁₀, and NH₃ available as reagent gasses)
• It can create and analyze both positive and negative ions
• Inert source reduces analyte decomposition during ionization
• Inlet:  Agilent 6890N gas chromatograph
• Mass analyzer:  single quadrupole
• Mass range:  m/z 1.6-800
• Mass accuracy:  ±0.2 Da
• Resolution:  unit (singly charged ion peaks ~0.7 Da wide)
• MSF owns the NIST 2002 EI mass spectral library (>170,000 spectra)
• Users can make their own mass spectral libraries

The Agilent 6890N is the inlet for the 5973 inert quadrupole mass spectrometer.  It is the larger box on the right-hand side of the photo.  The 6890 Series is the standard by which all other GCs are measured.  The GC-MS system is fully computer controlled with ChemStation software, thus programming of the flow rates temperature gradients are quite easy.  Look on the GC cabinet to find out which column and source are installed.  IUMSF owns a small number of GC columns (the default column is a 30 m long, 0.25 mm i.d., 0.25 um dF DB-5MS from Agilent, or something equivalent); users may provide their own columns if they wish.  The GC has a standard split/splitless injector and all gas flows are handled through the software.  Therefore, the split ratio may be varied with ease.  The 6890N is equipped with an autosampler and 100-position sample tray, enabling unattended recording of data.  It also ensures that all injections are reproducible, enhancing the ability to accurately quantify components in complex mixtures.

Be advised that this instrument is used by the A315 class in the fall (three afternoons per week all semester) and A314 in the spring (four afternoons during two weeks of the semester), so check ahead for availability during these times.

Training is available for users who wish to record their own data with this instrument.  Please contact Jonathan Karty or Angela Hansen to set up an appointment. 

Current rates for Chemistry Department users are $8.00/analysis for self-serve, $16 if MSF staff perform the analysis.

Please direct any questions concerning this instrument to Jonathan Karty or Angela Hansen.  (Back to top)

Waters/Micromass LCT Classic

Two instruments on indefinite loan from the laboratory of Dr. David Clemmer; originally purchased new in August 2005 by DEC.

The Waters/Micromass LCT Classic is an electrospray ionization/time-of-flight mass spectrometer (ESI-TOF).  The MSF has two of these instruments in A411.  The LCT next to the door (KC379) is set up for biomolecule analysis and has a Waters CapLC with autosampler as its inlet; its mobile phases are (A) 95% H₂O, 5% CH₃CN, 0.1% formic acid and (B) 95% CH₃CN, 5% H₂O, 0.1% formic acid; the column is a 0.5x150 mm  Agilent Zorbax SB300 C₁₈.  It is intended for walk-up LC-MS analysis of proteins using a ballistic 6 minute gradient.  The distribution of multiply charged ions can be interpreted using the ProTrawler software package from BioAnalyte.  Users may bring their own columns and solvents

The LCT next to the hood (KC366) is configured for high accuracy and small molecule measurements; it also has a Waters CapLC as its inlet.  The CapLC has three solvents (A is 95% H₂O, 5%CH₃CN, 0.1% formic acid; B is 95% CH₃CN, 5% H₂O, 0.1% formic acid, and C is HPLC-grade CH₃OH).  These solvents can be readily changed if necessary.  KC366 is also equipped with the LockSpray source which facilitates internal calibration for high precision work (e.g. formula matching for small molecules).  This instrument is typically set up for flow injection analysis of small organic molecules (no column installed and pumping straight solvent C) and is intended for walk-up MS of synthetic organic compounds.

The capabilities of the LCT in brief:

• Sources:  electrospray ionization (ESI), lock-spray electrospray ionization, atmospheric pressure chemical ionization (APCI)
• Inlets:  Waters CapLC, Agilent 1100 CapLC, direct infusion
• Mass analyzer:  orthogonal reflectron time-of-flight
• Mass range:  m/z 10-4,000
• Resolving power:  ~5,000
• Mass Accuracy
  • 50 ppm (external calibration)
  • 5 ppm (internal calibration)

Ideal solutions for ESI analyses include:

• aqueous 50% acetonitrile, 0.1% formic acid
• aqueous 50% methanol, 0.5% acetic acid
• 50% methanol, 50% chloroform
• aqueous 50% acetone, 0.1% formic acid
• aqueous 50% acetonitrile, 0.2% ammonia
• aqueous 50% acetonitrile, 2 mM ammonium acetate
• acetone or acetonitrile with 2 mM sodium acetate + 0.1% formic acid
• tetrahydrofuran may be used with some difficulty

Current rates for Chemistry Department users are $8.00/analysis for self serve, $16.00/analysis when MSF staff perform the analysis and $18.00 for a staff-run, accurate mass, formula matching analysis.  LC-MS with this instrument is $11 for self-serve and $25 if staff-run.

Please direct any questions concerning this instrument to Jonathan Karty or Angela Hansen.  (Back to top)

Thermo Electron Corporation MAT 95XP-Trap

Purchased new in March 2003 with funds from National Institutes of Health grant 1S10RR016657-01.

The MAT 95XP (manufactured by Thermo Electron Corp.) is our high resolution, high mass accuracy mass spectrometer.  It is typically used to analyze small organic compounds synthesized by Organic Chemistry faculty research groups.  It is an extremely versatile instrument with a variety of sources and inlets allowing staff to analyze everything from gasses to dendrimers.  Its high mass accuracy (< 5 ppm in magnetic sector scan mode aka BSCAN and < 2 ppm in electric sector scan mode aka ESCAN) enables its data to be used to provide formula matches.  That is, the mass spectra are precise enough to verify a chemical formula based on the sum of the mass defects from the constituent atoms.  This instrument also has an ion trap that can be used in place of the detector to allow up to 10 stages of tandem MS (MS^2-10) to be performed on ions isolated by its magnetic and electric sectors.  Its capabilities in brief:

• Sources:  electron impact (EI, variable energy), chemical ionization (CI, variable energy, choice of methane, isobutane, and ammonia as reagent gasses), fast atom bombardment (FAB), and electrospray ionization (ESI)  (note:  APCI is not currently available and the LCT is the preferred instrument for accurate mass ESI analyses)
• Inlets:  direct insertion probe, high temperature desorption probe, Trace gas chromatograph, direct infusion, FAB probe, and Agilent CapLC
• Mass analyzers:  double focusing magnetic sector - electric sector (reversed Nier-Johnson geometry B-E sector), 3D ion trap
• Mass range:  m/z 2-900 (high resolution EI/CI); 140-3,400 (high resolution ESI/FAB); m/z 2-3,500 (low resolution EI/CI/FAB/ESI); m/z 10-2000 (ion trap)
• Mass accuracy:
  • ±5 ppm (magnetic scan with internal calibration)
  • ±2 ppm (electric scan with internal calibration)
  • ±0.2 Da (ion trap)
• Resolving power:  up to 60,000 (5,000 is routinely used)
• Capable of online, high resolution GC-MS and LC-MS
• Capable of MS¹⁰ with online ion trap (ion trap has mass accuracy and resolution similar to other the quadrupole devices in the lab)

Current rates for Chemistry Department users are $18.00 per EI/CI analysis. 

Please direct any questions concerning this instrument to Jonathan Karty or Angela Hansen.  (Back to top)

Thermo Electron Trace Gas Chromatograph

(acquired as part of the MAT-95 XP Trap system)

The Thermo Trace GC is one of the many inlet systems available for use with the MAT-95 mass spectrometer.  The Trace GC is the box furthest to the left in the picture above.  This gas chromatograph has electronic pressure control so setting the split ratio for the injection is simple.  It has a split/splitless injector and is equipped with an Agilent DB-5 MS ((5%-phenyl)-methylpolysiloxane) 0.25 mm i.d., 0.25 µm df, 30 m long column (or something equivalent).  We often use this instrument to facilitate high resolution mass spectrometry of volatile samples.

High resolution GC/MS (EI or CI sources) with the MAT-95 costs $25.00/analysis.

Please direct any questions concerning this instrument to Jonathan Karty.  (Back to top)

Waters CapLC High Performance Liquid Chromatograph

(included with LCT purchase)

This HPLC was designed from the ground up for capillary-scale (<100 µL/min) analyses.  It has capillary scale pump heads and employs high pressure mixing for gradient generation.  Unlike the Agilent 1100, it does not require flow splitting for capillary flow rates.  It has three buffers (A is usually 95% H₂O, 5% CH₃CN, 0.1% HCOOH; B is usually 95% CH₃CN, 5% H₂O, 0.1% HCOOH, C is usually CH₃OH), and can create reproducible gradients with flow rates between 1 and 100 µL/min.  The CapLC can be equipped with a Waters 2487 dual wavelength UV-VIS detector and must be controlled by MassLynx or Waters HPLC software.  The MSF owns two which currently serve as the inlets for the LCTs.