Major Instruments

Dr. Bogdan Fedeles and Dr. Michael DeMott

MIT Building 16 Room 720

Tandem Triple 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 6530, situated down the hall from our primary location.   Our older model QTOF was retired last September do to age and to related power supply and rough pump problems, where repair costs would have outweighed any return on investment.  This newer model, equipped with a dual Agilent Jet Stream (AJS) electrospray source, offers a five- to ten-fold improvement in sensitivity over conventional ESI as found on our older instrument.  In addition, the corresponding HPLC stack contains newer Agilent 1290 components that provide better overall chromatography; and the computer offers updated software for data acquisition and analysis.  We are, therefore, grateful both to the Griffith Lab for agreeing to share their instrument and to the Tannenbaum Lab for hosting the instrument in their Mass Spec facility in 56-747.  As with other instruments, a Google calendar shows availability, but please contact Dr. Michael DeMott to arrange for training and scheduling.

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.

Q Exactive Orbitrap Mass Spectrometer

The Bioimaging and Chemical Analysis Facilities Core located in 16-720 purchased a Thermo-Fisher Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer last year and more recently added an EASY-nLC 1000 nanopump system. 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 this facility, the Q Exactive is paired with either a Dionex Ultimate 3000 UHPLC conventional LC that has a minimum flow rate of 20µl/min, or an EASY-nLC 1000 which allows nano-flow from 100-1000 nL/min.  Combined with a Thermo-Fisher Nanospray FLEX Ion Source, the latter system allows for detailed proteomics analysis.  These new capabilities are available since last month. For additional information or training on the Orbitrap instrument, please contact Dr. Michael DeMott (via the online inquiry form).

Additional Resource: DIY Capillary Column Packing

Recently, the core has acquired a Pressure Injection Cell device, sometimes called a “helium bomb loader”, to allow users to pack their own capillary columns for use with our ThermoFisher EASY-nLC 1000 nano-pump system.  No worries:  Our “bomb” does not explode, but instead provides controlled loading--using high-pressure helium gas--of nanobore capillary columns with solid-phase chromatography particles.  Self-packing saves money and allows detailed control over packing parameters such as column length, density, and solid-phase specifications.  Users must bring their own empty capillary columns and solid-phase beads, while we provide the device itself and all necessary accessories.  Again, please contact Dr. Michael DeMott for training.

Additional Resource: Nitrogen Generator

This core facility has also recently purchased a more efficient and environmentally friendly method for supplying nitrogen gas to all of the instruments in core lab 16-720, a Peak Scientific nitrogen generator paired with an Atlas Copco air compressor.  The new system removes the need for liquid nitrogen tanks—and all the expense and environmental strains caused by bi-weekly truck deliveries--by filtering nitrogen directly from our room air.  This eliminates almost 25 tank deliveries per year!  CEHS takes a stand for environmental health.   

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 is necessary before using the Agilent 7900 ICP-MS or the Milestone UltraWave microwave. Please contact Dr. Bogdan Fedeles (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.