At present, much of the work in proteomics is conducted with electrophoresis and 2-D gels.  This method will always play a part in proteomics research.  However, the volume of work that needs to be done also calls for methods and tools that offer greater speed and sensitivity.

Thermo Fisher Scientific believes that methods combining high-performance liquid chromatography and tandem mass spectrometry with an ion-trap instrument can produce rapid breakthroughs in proteomics.  For example, Thermo researchers recently analyzed a small sample of secreted proteins from Hep-G2 (human liver hepatoblastoma) cells during a five-hour period using the Thermo Scientific Surveyor™ Plus HPLC System and a Thermo Scientific LCQ™ Deca XP Plus ion-trap mass spectrometer.  The acquired results were then searched against an indexed human protein database using Bioworks software.  A total of 95 proteins was identified using these procedures.  By contrast, a Swiss study using more traditional methods with 2-D gels identified 25 secreted proteins from Hep-G2 cells.  Of these 25, the liquid chromatography/mass spectrometry method identified 24, plus many more.

Other researchers are also experiencing exceptionally good results using a combination of liquid chromatography and mass spectrometry instruments.  They include:

• Dr. Mark Duncan at the University of Colorado Medical School, who uses LC-MS-MS to determine proteins and peptides in tear drops.  He believes his line of inquiry will result in new diagnostic applications.  Typical analytical procedures have found about 50 peptides and proteins in teardrops; LC-MS-MS has found 500.                
• Dr. Steven Gygi of Harvard Medical School, who studies protein expression using a methodology called isotope-coded affinity that is supported by mass spectrometry.  He also studies protein interaction with mass spectrometry.                
• Dr. Donald Hunt of the University of Virginia, a leading researcher in using tandem mass spectrometry to understand peptides and the role they might play in immunology.                
• William S. Lane of Harvard University, who is an expert in protein identification software.             
• Dr. John Yates of Novartis Research Laboratories and the Scripps Research Institute, who operates an LC-MS system that can identify 2,400 proteins – a complete yeast genome – in 24 hours.

For information about Thermo Scientific products that support proteomics research, see the following:

Surveyor™ Plus HPLC System

TSQ™ Quantum™ Series

SEQUEST Cluster

Custom Peptides