Major Instruments

Dr. Michael DeMott and Dr. Stephen Slocum

MIT Building 16 Room 720

Tandem Quadrupole Mass Spectrometer

These instruments are ideal for targeted low-level quantification of compounds that ionize well in ESI (electrospray ionization) mode. ESI ionization efficiency is compound dependent, but for analytes that ionize well, the sensitivity can be high; routine detection levels of biomarkers of DNA or RNA modifications, for example, are in the low femtomoles. The basic technique is 'multiple-reaction monitoring' (MRM). For MRM experiments, ions of interest are selected in the first quadrupole (Q1), fragmented in the second quadrupole (Q2), and then fragment ions of choice are selected in the third (Q3). The two filters for chemical noise (in Q1 and Q3) usually result in a significant gain in signal-to-noise and consequent lower detection limits.

The Core facility in 16-720 houses one triple quadrupole mass spectrometers, an Agilent 6410, both with positive and negative ion capabilities.

Online resources:

Quadrupole Time-of Flight Mass Spectrometer (QTOF)

Quadrupole time-of-flights are high resolution instruments with mass accuracies in the low ppm range and can provide accurate masses for both molecular ions and fragment ions. For lower-molecular-weight analytes (e.g., below 600 da or so) it is usually possible to obtain reliable empirical formulas. For smaller proteins or nucleic-acid oligomers, the molecular weights can often be determined to within a dalton. These instruments are used extensively for proteomics, metabolomics, and biomarker discovery.
The Core has one QTOF system: an Agilent 6510.
The Agilent 6510 system has three different LC configurations:

  1. Agilent 1200 capillary LC system for 'standard' conditions, i.e., flow-rates ranging from 20 to 500/minute and columns with diameters from around .3 mm to 4 mm.
  2. Agilent 1200 capillary LC and Agilent 1260 Chip Cube interface. The latter configuration uses automatically-loaded microfluidic chips with on-chip trapping and analytical columns at flow rates in nL/minute ranges. It is primarily used for MS/MS analyses of protein digests.
  3. UPLC with an Agilent 1290 Infinity for fast chromatography.

Additional information:

Single Quadrupole Mass Spectrometer

This is a user-friendly combination of an Agilent 1100 LC and an Agilent single quadrupole mass spectrometer. As with the triple quadrupoles and the ion-trap, it has lower resolution and provides only nominal molecular weights. It is, however, robust and easy to use, so most preliminary studies, e.g., routine molecular-weight determinations, method development, and reaction progress evaluations are done with this system.

Thermo Fisher Orbitrap Q Exactive

The Bioimaging and Chemical Analysis Facilities Core located in 16-720 recently purchased a new Thermo Fisher Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer. From the company literature: “This benchtop LC-MS/MS system combines quadruple precursor ion selection with high-resolution, accurate-mass (HRAM) Orbitrap detection to identify, quantify and confirm more compounds rapidly and with confidence. The Q Exactive is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications, environmental and food safety, clinical research, and forensic toxicology where sensitivity and mass accuracy of small molecules is critical.” In our core facility, the Q Exactive is paired with a Dionex Ultimate 3000 UHPLC system with a conventional LC pump that has a minimum flow rate of 20µl/min, so proteomics analysis is currently not possible, but in the future we hope to acquire a nano-flow pump to expand the system’s capabilities. For additional information or training on the Orbitrap instrument, please contact Dr. Michael DeMott (via the online inquiry form).

Gas Chromatograph Mass Spectrometer











EI (electron ionization), PCI (positive chemical ionization) and NICI (negative ion chemical Ionization). In general, GC/MS is useful for analyzing volatile organic compounds, e.g., aliphatic hydrocarbons, polyaromatic hydrocarbons up to MW 300, pesticides , herbicides, fatty acids (after conversion to esters), and amino acids after derivatizing the acid and amine groups.

EI: After separation in the GC, molecules are ionized and fragmented with 70EV electrons. This energy is standard across virtually all GC/MS platforms, and EI Mass spectra are highly reproducible from laboratory to laboratory and therefore searchable against NIST/EPA/NIH mass spectral libraries, which significantly helps with identification of unknowns.

The relatively high energy of EI often produces mass spectra where the molecular ions are absent or of very low abundance. PCI and NICI sources operate with higher pressures of a reagent gas (usually methane) where the electron beam ionizes the reagent gas which then transfers charge to the analytes. These are much softer ionization methods that can produce molecular ions with much less fragmentation, and are therefore strongly complementary with EI.
PCI is thus used primarily for fragile molecules that do not yield molecular ions with EI. In addition, since the charge is distributed over fewer fragment ions, this often helps with sensitivity and detection of trace organic compounds.
NICI is the method of choice for detection and quantification of molecules with strongly electronegative substituents, e.g. F, Cl, I, Br or NO2 groups. Compounds are often derivatized with highly fluorinated derivatizing agents to enhance sensitivity in NICI.

Inductively Coupled Plasma Mass Spectrometry (ICP-MS): Agilent 7900












Agilent 7900 ICP-MS has a robust plasma with the new orthogonal detector system (ODS) which provide a wide dynamic range (up to 11 order of magnitude dynamic range) from sub-ppt to percent-level concentration therefore trace elements can be measure along with high concentration elements in the same run.

With the combination of the Milestone UltraWave microwave sample-digestion system, the CEHS core facility has capacity of analyzing geological samples. The CEHS core facility now has trace metal speciation capabilities by having a dedicated HPLC system for the Agilent ICP-MS system.
Prior training with Dr. Stephen Slocum is necessary before using the Agilent 7900 ICP-MS or the Milestone UltraWave microwave. Please contact Dr. Stephen Slocum (via the online inquiry form) to schedule a training time.

Liquid Chromatography

In addition to the LC/MS instruments listed above, the Core has two free-standing Agilent 1100 HPLC systems, both with diode array detectors (DAD). One is dedicated to method development, identification and quantification. The other, with a fraction collector, is primarily used for fractionation of trace biomarkers of DNA and RNA modifications, but could be configured for separations of other mixtures.