The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns.

Abstract

We describe here a computer system for the analysis of high-resolution two-dimensional gel-electrophoresis patterns, with some initial applications. The system (called TYCHO) comprises programs for image acquisition, background subtraction and smoothing, spot detection, gaussian spot modeling, and pattern matching and comparison. It is based on a conventional minicomputer, but makes extensive use of a high-speed array processor in the image-processing and -modeling steps. Used in concert with the ISO-DALT two-dimensional electrophoresis system (Anal. Biochem. 85:331-354, 1978), TYCHO allows quantitative measurement of hundreds of proteins in complex biological samples, and constitutes the initial data-reduction system required for work towards a Human Protein Index.

Gene and Protein Expression Profiles ofShewanella oneidensisduring Anaerobic Growth with Different Electron Acceptors

“…The 2-D gel images were digitized using an Eikonix 1412 charge-coupled device scanner interfaced with a VAX 4000-90 workstation. The images were then processed, and parameter lists (spot files) were generated using the Tycho II software developed at Argonne National Laboratory (Anderson et al, 1982). All spot files (two to three two-dimensional gel patterns per biological sample) were compared so that each matched spot in the patterns was numbered.…”

Effects of Toxic Agents at the Protein Level: Quantitative Measurement of 213 Mouse Liver Proteins following Xenobiotic Treatment

“…Since the protein is not reliably detected in untreated liver, it was not included in the set of 213 proteins initially chosen for study and its primary subcellular location was not revealed by subcellular fractionation experiments. We have called this protein Ibu: 1, in line with previous protein-mapping nomenclature (Anderson et aL, 1981).…”

“…This technology therefore has the potential to yield a much more comprehensive picture of protein effects than has been available previously. Through computer analysis of 2-D patterns (Anderson et al, 1981), it is possible to quantitate the abundance ofproteins quite accurately. More than 100 polypeptides can be measured on Coomassie blue-stained 2-D patterns of mouse liver proteins with coefficients of variation less than 15% (i.e., competitive with many enzymatic or immunochemical-specific protein tests) (Anderson et a!., 1985).…”

Paleoproteomics explained to youngsters: how did the wedding of two-dimensional electrophoresis and protein sequencing spark proteomics on: Let there be light

“…Of course antibodies were already a very powerful identification tool [20], but the huge gap between the abilities of 2D electrophoresis in terms of protein separation on the one hand, and the requirements of protein sequencing on the other hand, did not allow the protein scientists to answer the simple question: what is the protein that I see in this wonderfully changing spot ? Thus, 2D maps were very much looking as astronomical star maps, and it is not by chance that one of the first softwares used for the comparison of 2D gels was named from the Renaissance astronomer Tycho Brahe [21]. As the french philosopher Blaise Pascal wrote, "le silence éternel de ces espaces infinis m'effraie" (the eternal silence of the infinite spaces frightens me).…”