Shared Facilities Research

Proteomics & Mass Spectrometry Core

Scientific Director:  Bruce Stanley, PhD

An Applied Biosystems 4700 Proteomics Analyzer (MALDI TOF-TOF), an MDS Sciex 4000 QTrap, and a reflectron, delayed extraction MALDI-TOF mass spectrophotometer (Voyager DE-PRO, Perseptive Biosystems/Applied Biosystems) are available for protein, peptide, oligonucleotide and small molecule analyses. In addition to 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 f or 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.

Unknown proteins can be further characterized by partial sequence determination of proteolytic fragments using tandem MS/MS ion fragment analysis. Additional analyses (e.g., partial sequence determination utilizing Collision-induced Dissociation (CID) fragmentation analysis with MALDI TOF-TOF are available. 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:

·         ABI 4700 Proteomics Analyzer MALDI TOF-TOF MS

·         MDS Sciex 4000 QTrap hybrid ion trap MS

·         ABI Voyager DE-PRO Reflectron MALDI TOF MS

·         Phenyx advanced protein-MS ID software; GPS Explorer and Mascot software

·         Eksigent 2D nanoLC liquid chromatography system

·         LC Packings/Dionex ProBot MALDI spotting robot

·         ABI BioCad LC system

·         Beckman-Coulter PF 2D Protein separation system

·         Shimadzu CHiP printer

·         LEAP Technologies 2DiDx Spot-cutting/digestion/spotting