Mass Spectrometry

Mass Spectromertry Center

The Mass Spectrometry Center

The Center for Mass Spectrometry (CMS) facility at The Merkert Chemistry Center maintains a wide range of state-of-the-art mass spectrometers and chromatographic systems, providing the full suite of ionization and separation options that are capable of dealing with all sample types and a wide array of client demands. Ionization methods available include ESI, APCI, APPI, DART, and AP-MALDI, all of which are capable of operating in both the positive and negative ion modes.

Samples are generally run by the facility staff, and the results are provided as electronic data files. In special circumstances, an individual researcher who makes frequent use of a particular spectrometer may receive training and become authorized to run samples personally. Such authorized users then often run samples for other members of their own research group to reduce the pressure on the facility staff.

If you are an external user seeking to use Merkert CMS facilities, please contact Mr. Marek Domin to discuss your project.

Complete Facility Description

1. Advion Expression CMS

TThe expression CMS is a single quadrupole mass spectrometer, equipped with ESI and APCI probes, switchable with minimal effort.

The instrument has a mass range of m/z 10 to m/z 1,200, and a resolution of 0.5-0.7 m/z, units at 1000 m/z, over the entire acquisition range.

In Full scan mode the CMS has sensitivity for Reserpine of 100pg and in SIM mode of 10pg, with a 5μl sample injection volume of 100μl/min.


The JEOL AccuTOF, configured with a new Direct Analysis in Real Time (DART) ion source, represents a significant breakthrough in mass spectrometry. It is the first mass spectrometer to allow the analysis of solids, liquids and gaseous samples at atmospheric pressure and ground potential by simply placing the sample between the DART and the mass spectrometer. No solvents or sample preparation are required. The system design results in high throughput with no carry over, even with neat polyethylene glycol (PEG). The DART can even analyze samples directly from a variety of surfaces such as concrete, currency, food, pills, clothing, and TLC plates. The AccuTOF DART combination achieves high specificity through high resolution. Exact mass measurements together with precise isotopic abundances can rapidly identify unknown compounds by their elemental compositions.

The DART ion source is based on the reactions of excited-state species with reagent molecules and polar or non-polar analytes. It is free of the limitations that are common to other atmospheric pressure ion sources, which require direct exposure of gaseous or vaporized liquid samples to elevated temperatures and electrical potentials, ultraviolet irradiation, laser radiation, or a high-velocity gas stream. DART does not alter the sample in any way, nor does it expose the user to a potentially harmful substance or dangerous situation.

DART Applications

3. Agilent 6220 Time-of-Flight LC/MS

The Agilent 6220 TOF LC/MS delivers exceptional analytical performance, including 2-ppm mass accuracy, and is ideal for protein and metabolite profiling. The powerful combination of resolving power and high mass accuracy allows identification of impurities in complex matrices faster and with greater confidence than with other methods. The instrument has a variety of ion source ESI, APCI, APPI and AP-MALDI meeting the widest range of applications.

The atmospheric pressure photoionization (APPI) source is especially useful for analyzing compounds that ionize poorly by ESI and APCI. It uses a krypton lamp that emits photons at energy levels high enough to ionize compounds with a UV chromophore, but low enough to minimize the ionization of air and common HPLC solvents. Relatively low ionization energy means the APPI source causes minimal fragmentation and generates mostly molecular ions and protonated molecules.

The atmospheric pressure matrix assisted laser desorption ionization (AP-MALDI) source provides fast, easy, and ultrasensitive analysis for samples that do not need online separation. It is ideal for protein identification and confirmation using peptide mass fingerprinting (PMF).

Coupled to the mass spectrometer, a 1200 series rapid resolution LC system offers a unique combination of flexibility, resolution and speed. Benefits include the ability to run both rapid resolution and conventional HPLC methods on the same chromatography system, which supports both standard and narrow bore columns. Rapid resolution, in turn, offers up to 60% higher resolution than conventional HPLC, with approximately 20 times faster analysis time, compared to standard HPLC.

4. Agilent 6460 Triple Quad

The 6460 Triple Quad MS is a liquid chromatograph triple quadrupole mass spectrometer that performs MS/MS using three sets of parallel rods (in this case, quadrupole, hexapole, quadrupole). The first quadrupole separates ions into precursor ions that are fragmented in the hexapole into product ions, which are separated by the second quadrupole. Often, two or more precursor ions and their product ions are monitored in sequence in MRM (multiple reaction monitoring) mode. You can monitor up to 4000 MRM transitions by using Dynamic MRM.

Marek Domin

Marek Domin, MSc FRSC CChem CSci
Director, Mass Spectrometry Center

Mr. Marek Domin joined the Chemistry Department at Boston College in August 2005. A native of England, Mr. Domin worked at the School of Pharmacy in London for ten years as part a large mass spectrometry group. He obtained his M.Sc. degree in chemical research from Birkbeck College, where he used capillary electrophoresis, as an alternative to gas chromatography – mass spectrometry for the detection of modified DNA bases by hydroxyl radicals. During his graduate studies, he carried out research into the characterization of micro-organisms using MALDI-TOF. Mr. Domin’s research interests include the application of mass spectrometry as a routine tool for chemistry/chemical biology; exploring new research applications for mass spectrometry; reaction monitoring by mass spectrometry; and the use of open air ionization methods for the analysis of pharmaceutical, biological, and chemical analysis.

“Ambient Ionization Mass Spectrometry” edited by Marek Domin

Link to Publications

Mass Spectrometry Center
Marek Domin, M.Sc.
Merkert Chemistry Center
2609 Beacon Street
Chestnut Hill MA 02467-3808
Work: 617.552.3077
Mobile: 617-895-7739