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Protein Facility

News

August 11, 2009
Facility acquires Progenesis SameSpots software from Nonlinear Dynamics for analysis of 2D gels

April 14, 2008
The amino acid analysis service has been discontinued, see here for details.

Typhoon imaging system and the 2D gel documentation/analysis system

The facility has two methods for the acquisition of digital gel images. For the acquisition of Coomassie Blue stained gels, the Amersham Pharmacia Biotech ImageScanner flatbed scanner with transparency module can be used. Once the gel image has been digitized, 2-D gel analysis can be performed using Progenesis SameSpots from Nonlinear Dynamics.
SameSpots allows for the alignment and analysis of 2D gels in a short amount of time and returns data that shows the expression of proteins under different biological conditions. The software presents a list of the most significantly changing spots within a set of gels, allowing for the rapid screening of protein spots that may be of the most interest in a set of gels. These spots can then be further analyzed by other equipment in the Protein Facility (trypsin digestion followed by peptide mass fingerprinting or internal sequencing, direct N- terminal sequencing of the blotted gels). SameSpots uses pixel-level alignment that allows for 100% spot matching. This eliminates missing values and reduces the need for spot-editing. Each spot on a set of gels will use the same spot outline making comparisons of replicate gels under different conditions much easier and more accurate.
An older software package (PDQuest from Bio-Rad) is also available.

The Typhoon 8600 from Amersham Pharmacia Biotech is a multimode image scanner that can be used for the acquisition of phosphorescence, fluorescence or chemiluminescent samples. The scanner is capable of imaging gel sandwiches, agarose and polyacrylamide gels, membranes, microplates and microarrays. Samples can also be labeled with multiple dyes and imaged on the Typhoon. After image acquisition, the image can be analyzed for quantitative data using ImageQuant software from Amersham Pharmacia Biotech.