Search Engine for Proteomics: Fact or Fiction? (Part 2)

Adequate processing of the results of a large-scale experiment, e.g. proteomics analysis, requires interpretation tools acting on a similarly large scale. The most desired interpretation mode is the pathway analysis, i.e. answering the question which signaling and metabolic pathways are activated in the sample compared to a control. In order to provide reliable, unbiased pathway analysis, a bioinformatic tool is required that integrates three elements: i) the pathway database; ii) the mapping tool converting the input data (protein IDs and their abundances) into the elements of pathways, and iii) the scoring system for pathways. These inherent attributes of the Pathway Search Engine (PSE) make it similar to Web search engines, e.g. those provided by Google, Yahoo!, etc. Here we report on the development of a PSE prototype and on its possible applications in proteomics, biology and medicine.