The CIT houses state-of-the-art omics instrumentation and technology and our multi-vendor approach allows for highly customizable, flexible applications that can be tailored to our client’s specific needs.

Instrumentation includes:

  • four LC-ion mobility mass spectrometers
  • one high resolution LC-Orbitrap mass spectrometer
  • one LC-QqQ (triple quadrupole) mass spectrometer

This omics instrumentation is supported by a variety of sample handling accessories including autosamplers, ultra high performance liquid chromatography (UHPLC), supercritical fluid chromatography (SFC), and a nanoflow ChipCube platform.

Importantly, the CIT (in conjunction with the McLean laboratory) is designated as a Waters Center of Innovation (Waters Corporation) and recognized as an Agilent Thought Leader laboratory (Agilent Technologies).

Mass Spectrometry Sample Vials

Liquid chromatography-mass spectrometry (LC-MS) tandem instruments offer the ability to separate compounds by both polarity (LC) and mass-to-charge (MS) ratio dimensions. A range of chromatography methods including reverse phase liquid chromatography (RPLC) and hydrophillic interaction liquid chromatography (HILIC) can be used to optimize stationary phase retention.


The CIT houses several commercially available liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) instruments. These instruments offer the ability to separate ions or metabolites in three dimensions: polarity (LC), molecular size/shape/charge (IM), and mass-to-charge (MS). All instruments are optimized for sensitivity to low molecular weight analytes (<2000 Da). Both traveling wave ion mobility-mass spectrometry (IM-MS) instruments (Synapt G2 HDMS and Synapt G2-S HDMS models, Waters Corporation) are coupled to Acquity UPLC or nanoAcquity UPLC systems. The G2-S HDMS model incorporates StepWave ion transfer optics and TriWave IM technologies for increased sensitivity. Both, Synapt nano- and conventional electrospray ionization (ESI) utilize a lockspray, which allows for mass calibration during data acquisition. In addition, a quadrupole using a collision-induced dissociation (CID) cell both directly before and after the traveling wave mobility cell can perform mass selection and fragmentation.

The CIT also houses two state-of-the-art Agilent ion mobility instruments (Model 6560). These instruments were built with enhanced drift tube ion mobility resolution and precision. The 6560s are coupled to either a binary LC system (1260 Infinity, Agilent) or a nano flow LC (Chip Cube capabilities) that utilizes columns or prepackaged chips (Chip Cube) for enhanced reproducibility. The dual jet stream source is an electrospray ionization (ESI) source for increased sensitivity capabilities. For more specialized analyses, the static field ion mobility cell is capable of running in numerous gas conditions (i.e., nitrogen, helium and carbon dioxide) depending on the user’s needs.

Example Applications: lipidomics, chiral separations, structural characterization, biological and environmental analyses, xenobiotics, exposomics, environmental health (water testing)

Orbitrap LC-MS

The CIT houses one state-of-the-art LC-HRMS omics instrument: the Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific). This instrument combines a segmented quadrupole for high-performance precursor ion selection with a high-resolution and accurate-mass (HR/AM), ultra-high-field Orbitrap mass analyzer offering a combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity.

Our QE-HF is equipped with an ultra-high performance liquid chromatography system (Vanquish, ThermoFisher Scientific), nano- and conventional electrospray ionization (ESI) sources.

Example Applications: drug metabolites, biotechnological samples, and environmental toxins – even in complex matrices

Triple Quadrupole LC-MS

For targeted analysis experiments (mainly multiple reaction monitoring (MRM), dynamic MRM (dMRM), and triggered MRM (tMRM)), the CIT is utilizing an Agilent 6470 Triple Quadrupole (QqQ) LC/MS system. The components of this tandem system include two mass filters and a collision cell, enhanced ion optics and detector design over other systems allowing for attogram level sensitivity for specified analytes.

Through its increased sensitivity, wider linear range, and better signal-to-noise ratios it allows for lower detection limits. This instrument can perform either relative or absolute quantification of small molecules of interest.

Generally, global untargeted analyses precedes targeted analysis experiments, unless specific metabolic pathways or metabolites (i.e., TCA cycle, carnitine biosynthesis, amino acids, redox/energy molecules) are of interest to the user.

Example Applications: metabolites, drugs, lipids, peptides, amino acids, and canonical metabolic pathways of interest for biomarker validation, pharmaceuticals, steroids, toxicology/environmental analyses, and forensics