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New Extraction Methods Open Up FFPE Tissues


A vast reserve of proteins exists within tissues that have been fixed in formalin and embedded in paraffin, but these proteins have been too difficult to extract for most large-scale proteomics experiments. Two new technologies have recently been developed, however, that could change the way proteomics researchers look at preserved tissues. The methods, from the University of Utah School of Medicine and the company Expression Pathology, enable proteins to be extracted and solubilized in a large-scale manner, and then identified by mass spectrometry.

A team of researchers led by Kojo Elenitoba-Johnson, the director of molecular hematopathology and proteomics at the University of Utah School of Medicine, described one technique for extracting and analyzing proteins from formalin-fixed paraffin-embedded (FFPE) material in a paper published Sept. 5 in Laboratory Investigation.

Elenitoba-Johnson and his team first removed paraffin from the preserved sample by passing it through a number of solvents. They then used enzyme digestion to liberate proteins that had been crosslinked to DNA through formalin fixation. The liberated peptides were analyzed by mass spectrometry.

“We used a bottom-up approach,” Elenitoba-Johnson explains. “We decided to do a protein digestion, then analyze the peptides and track them back to the databases. In terms of large-scale identification of proteins extracted from paraffin, I think ours would be considered one of the more comprehensive search approaches.”

Aside from Elenitoba-Johnson’s method, a commercialized kit has also been developed to extract and analyze FFPE proteins in a relatively high-throughput manner.

The kit, developed by Expression Pathology, extracts proteins and nucleic acids from formalin-fixed tissue using the company’s patented Liquid Tissue Protein formula. Next, cells are heated, causing proteins to be “shot out” of the sample. The resulting solution can then be analyzed using mass spec or other techniques.

— Tien-Shun Lee



US Patent 6,950,754. Apparatus and method for automated protein design. Inventors: Stephen Mayo, Bassil Dahiyat, Benjamin Gordon, Arthur Street, Yaoying Su. Assignee: California Institute of Technology. Issued: September 27, 2005.

This patent covers methods for “quantitative protein design and optimization … [based on] receiving a protein backbone structure with variable residue positions, establishing a group of potential rotamers for each of the variable residue positions … and analyzing the interaction of each of the rotamers with all or part of the remainder of the protein backbone structure to generate a set of optimized protein sequences.”


US Patent 6,949,739. Ionization at atmospheric pressure for mass spectrometric analyses. Inventor: Jochen Franzen. Assignee: Bruker Daltonik. Issued: September 27, 2005.

“The invention provides a lengthy ion mobility drift tube with a focusing electric field inside to guide the ions from an ionization cloud generated at atmospheric pressure towards the entrance opening of the mass spectrometer,” according to the abstract.


The Structural Genomics Consortium, a charity funded with $95 million by pharmaceutical and government organizations, has added a research center at the Karolinska Institute in Sweden to its two facilities at the University of Oxford and the University of Toronto. The new laboratory plans to determine at least 50 new protein structures of biomedical importance in the next two years. SGC kicked off in July 2004 and its researchers determined 78 novel protein structures in its first year of operation.


Proteomic Solutions, a protein laboratory service and reseller of proteomics products based near Paris, will distribute Geneva Bioinformatics’ Phenyx mass spectrometry analysis software throughout France. Phenyx, developed with the Swiss Institute of Bioinformatics, is used to identify and characterize proteins and peptides from mass spectrometry data.


Epitome Biosystems and EMD Biosciences signed an agreement to develop products based on Epitome’s EpiTag technology. Epitome will develop reagents for the quantitative measurement of key intracellular signaling proteins.


NCI expects to issue two RFPs this fall as part of its Clinical Proteomic Technologies Initiative. One will establish the Clinical Proteomic Technology Assessment Consortia, and the other aims to support investigator-initiated proteomics projects.



$1.5 million

Case Western Reserve University’s School of Medicine won a three-year, $1.5 million grant to support the Case Proteomics Center. The center is currently seeking a well-known leader and 10 to 14 scientific researchers. The grant will go toward salaries and major equipment purchases.


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