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Mass Spectrometry

Mass Spectrometry

Chemical Characterisation / Tissue Imaging Unit

The Mass Spectrometry Facility in the School of Chemistry provides MS services for School and associated researchers, and is now a part of the CMAP initiative as the 'Chemical Characterisation / Tissue Imaging' unit.

The Chemical Characterisation / Tissue Imaging unit is open to SFI and non-SFI researchers from the School and externally, to industry, and other national and international users.

In 2020 our MS instrumentation suite was upgraded, with the addition of modern Agilent and Bruker systems.
This augments our existing Waters instrumentation which has provided many years of analysis for the School of Chemistry and associated researchers.

This was made possible through The Comprehensive Molecular Analysis Platform (CMAP) initiative under The  (opens in a new window)SFI Research Infrastructure Programme in 2019, reference 18/RI/5702, and (opens in a new window)BiOrbic, the SFI Bioeconomy Research Centre, and with the support of the School of Chemistry and UCD.
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Agilent 6546 Quadrupole Time-Of-Flight MS System

QTOF LC 1260InfinityPrimeII Agilent 6546 QTOF System

This system is equipped with an Agilent 1260 Infinity Prime II LC system capable of delivering pressures of 800 Bar.

The Agilent 6546 is a latest-generation Q-ToF system and is the first of its kind to be delivered in Ireland. The technologies incorporated in this system afford the capability to simultaneously obtain high speed, high resolution, and wide dynamic range without data quality sacrifices.
Building on previous generations of source development, ion rail technological improvements and iterative software advancements, with the 6546 we can obtain:

  • Confidence in identification, with exceptionally low false positives/ negatives
  • The ability to detect more compounds in a single analysis
  • Stability in response over many samples
  • Software to rapidly turn MS data into reliable answers
  • The ability to handle large quantities of data simultaneously 

It is expected that this system shall facilitate the delivery of contemporary techniques in the HRAM (high-resolution accurate mass) analysis of a range of species ranging from small to intermediate sized molecules of synthetic and biological origin.

For further details on the capabilities of this instrument please see the following link:
(opens in a new window)https://www.agilent.com/cs/library/brochures/brochure-6546-q-tof-5994-0686en-agilent.pdf

Agilent Single-Quadrupole LCMSD-XT

Agilent SQ MS

This system is a nominal mass single quadrupole mass spectrometer with fast polarity switching and an extended range capability. It is primarily intended for walkup nominal mass analysis and quantitative projects where single-ion monitoring is appropriate. 
This system is equipped with an Agilent 1260 HPLC system capable of up to 600 Bar with a dedicated 100-position autosampler and addition wavelength detection and fraction collector.

For further information please see:
(opens in a new window)https://www.agilent.com/en/product/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-instruments/single-quadrupole-lc-ms/lc-msd-xt

Bruker 'autoflex maX' MALDI system with MALDI Imaging Platform

MALDI Autoflex Max 300

The Bruker AutoFlex MAX system is an advanced MALDI (Matrix Assisted Laser Desorption Ionisation) TOF/TOF platform with advanced laser and ion optic subsystems and Bruker's state-of-the art vacuum technologies.

The AutoFlex Max platform is noted for:

  • Simplicity: The autoflex maX series takes advantage of the straightforwardness of MALDI-TOF for LC-free mass spectrometry. The analytical needs of quality control and target characterization of biopharmaceuticals, glycans, and polymers can be readily addressed.
  • Speed: With a laser repetition rate up to 2 kHz, higher throughput workflows including product integrity screening or thin layer chromatography coupled to MALDI are rapidly executed, and molecular imaging studies – from tissue slices to plants and beyond – can be made within practical laboratory timeframes.

The system is suitable for samples of synthetic and biological origin including proteins, oligosaccharides, polymers, organometallics and other species.

For further information see the following link:
(opens in a new window)https://www.bruker.com/content/bruker/int/en/products-and-solutions/mass-spectrometry/maldi-tof/autoflex-max.html 

The UCD system comes with a (opens in a new window)HTX Technologies TM-Sprayer for preparation of MALDI-Imaging samples, along with (opens in a new window)SCiLS Lab software for advanced data analysis and visualisation of MALDI Imaging data. 

Other Equipment

The MS lab also has a Waters/Micromass LCT High-resolution Accurate Mass system, a Waters/Micromass Quattro Micro QqQ system and a GCT Premier GC-MS system.

The Chemical Characterisation Suite offers services in High-resolution quantitative and qualitative analysis of samples of synthetic and biological origin, and our services are available to SFI and non-SFI researchers, and Industry. 

Our instrumentation offering is underpinned by a suite of software and databases which includes:


  • MassHunter Qualitative Analysis
  • MassHunter Quantitative Analysis
  • BioConfirm
  • PCDL
  • BioConfirm
  • Mass Profiler
  • Lipid Annotator
  • ProFinder


  • FlexControl
  • FlexAnalysis
  • FlexImaging
  • BioPharmaCompass 3
  • SCiLs


  • MassLynx

    For further information please see the Bookings section.

Contact UCD School of Chemistry

University College Dublin, Belfield, Dublin 4, Ireland.
T: +353 1 716 2132 / 716 2425 | E: chemistry@ucd.ie