The Proteomics Facility is a full service facility employing high throughput state of the art chromatography-electrospray mass spectrometry for proteomics analysis. We offer a wide range of services for our clients as outlined below. These services range from advanced preparative HPLC and processing of complex protein mixtures to single gel spot digest analysis. Mass spectrometry analysis is by 1D and or 2D-LC-MS/MS. Analysis of data for post-translational modifications, protein profiling, and protein ID are also available.

Raw sample processing and protein extraction and preparation from:

• Urine
• Plasma/serum
• Cell culture supernatants
• Cultured cells
• Tissues

Protein/peptide Purification

•  Analytical and preparative 1D native and SDS PAGE
•  Affinity purification
•  HPLC separation/purification(AKTA EXPLORER
  • Size Exclusion
  • Ion exchange
  • Reverse phase
  • Hydrophobic interaction

Protein Identification(4 LCQ-DecaXP Plus, 1 LTQ-FT)

•  Protein from solution, 1D and 2D gels
•  Post translational modification identification

Protein Biomarker Discovery

• Plasma, cells, tissues

Specialty subproteomic purification for biomarker discovery

• Glycoprotein, purification, analysis and profiling
• Phosphoprotein/phosphopeptide analysis
• Protein degradation products(degradomics)

 

The Proteomics core provides researchers with protein biochemistry and mass spectrometry resources in support of research projects. The goal of the core is to provide information on both the qualitative and semi-quantitative protein content and protein modifications using the latest and most robust technology available. We have four ThermoFinnigan LCQ Deca XP plus mass spectrometers, which can be equipped to run with microspray sources with the Proteome X system or with nanospray sources. The LC/MS units are configurable to process both 1-D and 2-D liquid chromatography inputs both in microspray and nanospray modes.

• LTQ-FTMS system and 4 DecaXP plus Proteome X workstations
  • 4 Microspray sources, 1D/2D
  • 5 Nanospray sources, 1D/2D
  • Column packing consumables and equipment for both nano and microspray capable columns.
  • AKTA Explorer workstation

Other equipment available are a high capacity-high vacuum speedvac for lyophilizing samples in plate format, and a bio-safety cabinet to minimize unwanted environmental contamination of samples and permit safe handling of samples such as human source fluids, tissues, or cell/microbial cultures.

• Gel electrophoresis equipment
• Tissue processing equipment(Polytron, probe sonicator, tissue grinder)
•  High vacuum concentrator
  • 20/8/4 MTP capacity
• 2 Single, 1 Dual, 1 Quad CPU workstation+(10node cluster)

Ion traps identify proteins by taking a single protein or mixture of proteins and digesting them down to smaller components(peptides), using an amino acid specific protease.  These smaller peptides are then separated by hydrophobicity on a liquid chromatography column, the eluant from which is “sprayed” into the front of the mass spectrometer by applying a high voltage to the tip of the column.  Simple mixtures of peptides that elute get sprayed into the MS are then “trapped” in the center of the machine and scanned out by their mass to charge ratio into a detector.  Peptides that are detected by the MS are then selected,  fragmented, and the fragments scanned out of the trap.  Peptides break cleanly at their amide bonds yielding a ladder of ions, the spacing of which corresponds to single amino acid masses.  The “ladders” from the mass spectrometer are then compared against theoretical protein databases and the sequence of the peptides can be determined and matched to a protein.  In this manner, complex mixtures of proteins can be rapidly identified.