Core facilities proteomics


Proteomics Core Facility

The NICB’s Proteomics Core Facility is well equipped with instrumentation for protein identification, characterization and quantitation. The NICB is equipped with high end proteomics and mass spectrometry equipment which is supporting many research programmes in the NICB as well as providing proteomics input to several non-NICB programmes in DCU and externally, and to 3U researchers.

The proteomics facility is equipped with instruments for quantitative liquid chromatography mass spectrometry profiling approaches such as quantitative label-free LC-MS. The mass spectrometry equipment includes an LTQ Orbitrap XL which is capable of high mass resolution and accurate mass determination, and an LTQ XL equipped with ETD (Electron Transfer Dissociation). ETD allows peptide fragmentation while preserving post translational modifications such as phosphorylation. The facility also houses a 4800 Plus MALDI TOF TOF for high throughput MALDI MS/MS analysis. The facility also houses equipment and software for 2D gel electrophoresis (IPGphor, Ettan Dalt 6 and 12 tanks, Typhoon 9400 fluorescent imager), including 2D Difference Gel Electrophoresis (2D DIGE) where samples can be differentially labelled with fluorescent dyes (e.g. Cy2, Cy3, Cy5). There is also the capability of performing routine 1D LC-MS/MS for simple protein/peptide mixtures (e.g. from 1D or 2D gels) as well as 2D LC-MS/MS for complex protein/peptide mixtures. There is also the capability to quantify peptides/proteins in biological samples using a TSQ Vantage Triple Quadrapole mass spectrometry for SRM/MRM applications.

Learn more about the NICB's research on the Proteomics of Biopharmaceutical production cells here.


Paula Meleady (

Michael Henry (



Mass Spectrometry Equipment

  • LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific)
  • LTQ XL mass spectrometer equipped with ETD  (Thermo Fisher Scientific)
  • 4800 Plus MALDI TOF TOF mass spectrometer (AB Sciex)
  • TSQ Vantage Triple Quadrupole for quantitative SRM/ MRM applications (Thermo Fisher Scientific)
  • Equipment and software for 2D Difference Gel Electrophoresis (2D DIGE)
  • Luminex xMAP system for multiplex ELISA
  • Ultimate 3000 RSLCnano systems (Dionex/Thermo Fisher Scientific) x 3
  • IPGphor (GE Healthcare) x 3 units
  • Ettan Dalt 6 SDS PAGE tank (GE Healthcare) x 1 unit
  • Ettan Dalt 12 SDS PAGE tank (GE Healthcare) x 3 units
  • Typhoon 9400 fluorescent scanner (GE Healthcare)


  • MASCOT (Matrix Science)
  • Proteome Discover (Thermo Fisher Scientific)
  • Progenesis QI for Proteomics (NonLinear Dynamics)
  • SIEVE (Thermo Fisher Scientific)
  • SEQUEST/Bioworks (Thermo Fisher Scientific)



  • Dowling P, Pollard D, Larkin A, Henry M, Meleady P, Gately K, O'Byrne K, Barr MP, Lynch V, Ballot J, Crown J, Moriarty M, O'Brien E, Morgan R, Clynes M. (2015) Abnormal levels of heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) in tumour tissue and blood samples from patients diagnosed with lung cancer. Mol Biosyst. 2015 Mar;11(3):743-52


  • Ravidà A, Musante L, Kreivi M, Miinalainen I, Byrne B, Saraswat M, Henry M, Meleady P, Clynes M, Holthofer H. Glycosylation patterns of kidney proteins differ in rat diabetic nephropathy. (2015) Kidney Int. 2015 May;87(5):963-74.


  • Linge A, Maurya P, Friedrich K, Baretton G, Kelly S, Henry M, Clynes M, Larkin A, Meleady P. (2014) Identification and functional validation of RAD23B as a potential protein in human breast cancer progression. J. Proteome Res. 2014 Jul 3;13(7):3212-22.


  • Meleady P, Gallagher M, Clarke C, Henry M, Sanchez N, Barron N, Clynes M. (2012) Impact of miR-7 over-expression on the proteome of Chinese hamster ovary cells. J Biotechnol. Aug 31;160(3-4):251-62.



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