Proteomics and Mass Spectrometry Core

Director:  Bruce Stanley, Ph.D
Phone: 717-531-5329

Senior Research Support Associate: Anne Stanley, D.U.T. (IUT de Strasbourg)
Phone: 717-531-6087

Assistant Professor: Gang Chen, Ph.D.
Phone: 717-531-1075

Research Associate: Jenny Dai, MS
Phone: 717-531-0003 extension 287146


ABSciex 5600 TripleTOF, Applied Biosystems 5800 MALDI TOF-TOF, a Waters Synapt HDMS, an MDS-Sciex 4000 QTrap, and a reflectron, delayed extraction MALDI-TOF mass spectrophotometer (Voyager DE-PRO, Perspective Biosystems/Applied Biosystems) are available for protein, peptide, lipidomic, oligonucleotide and small molecule/metabolomic analyses. In addition to simple uses for quality control assessment of synthetic peptides and oligonucleotides, the mass specs can be used for analyses of complex mixtures of peptides, for example from proteolytic digests of proteins purified by column chromatography, by metal affinity chromatography, by SDS-PAGE or 2D gel electrophoresis, or from PVDF/nitrocellulose membranes, with a microliter of sample at micromolar concentrations sufficient for analysis. These types of analysis can be used, for example, to detect and analyze phosphoproteins and other post-translational modifications, for isozyme analysis, and for identification of unknown proteins. For example, a typical proteomic experiment can currently identify between 2,000-4,000 proteins from a single sample, or simultaneously identify and provide relative quantitation for 500-2000 proteins from up to 8 samples.

Nanospray ionization, electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), or photoionization can be implemented to analyze samples ranging from peptides to lipids to oligonucleotides to small molecules. Additionally, multiplexed antibody western blot analysis and on-blot digestion can be performed to further aid in identifying and characterizing proteins.

Services Offered: 

  • Mass Spectrometry analyses and identification of proteins, peptides, oligonucleotides, carbohydrates, small molecules
  • 2D LC separations of complex protein and/or peptide mixtures for Proteomics
  • Protein Expression analysis using ICAT & iTRAQ methodology
  • Protein Expression analysis using 2D Gel-image analysis
  • Automated spot-cutting, proteolytic digestion, and sample deposition from gels
  • Shared equipment for analyzing whole protein sizes and multimeric state

Major Equipment:

  • ABSciex 5600 TripleTOF MS (Nanospray and ESI)
  • Applied Biosystems 5800 MALDI TOF-TOF
  • MDS Sciex 4000 QTrap hybrid ion trap MS
  • Waters Synapt HDMS Ion Mobility Mass Spec
  • ABI Voyager DE-PRO Reflectron MALDI TOF MS
  • ProteinPilot, Phenyx, and Mascot advanced protein-MS ID software
  • Tempo LC-MALDI nanoLC liquid chromatography system and MALDI spotting robot
  • Akta biocompatible LC system and serum clean-up system
  • Eksigent ChipLC Nanoflow HPLC
  • Waters Acquity and NanoAcquity UPLC systems
  • Beckman-Coulter PF 2D Protein separation system
  • Shimadzu CHiP printer
  • LEAP Technologies 2DiDx Spot-cutting/digestion/spotting
  • Wyatt DAWN HELEOS light-scattering detection system for protein sizing

Click Here to visit the Proteomics and Mass Spectrometry Core website.