Abstract
Proteomics inherently deals with huge amounts of data. Current mass spectrometers acquire hundreds of thousands of spectra within a single project. Thus, data management and data analysis are a challenge. We have developed a software platform (Proteinscape) that stores all relevant proteomics data efficiently and allows fast access and correlation analysis within proteomics projects. The software is based on a relational database system using Web-based server-client architecture with intra- and Internet access. Proteinscape stores relevant data from all steps of proteomics projects—study design, sample treatment, separation techniques (e.g., gel electrophoresis or liquid chromatography), protein digestion, mass spectrometry, and protein database search results. Gel spot data can be imported directly from several 2DE-gel image analysis software packages as well as spot-picking robots. Spectra (MS and MS/MS) are imported automatically during acquisition from MALDI and ESI mass spectrometers. Many algorithms for automated spectra and search result processing are integrated. PMF spectra are calibrated and filtered for contaminant and polymer peaks (Score-booster). A single non-redundant protein list—containing only proteins that can be distinguished by the MS/MS data—can be generated from MS/MS search results (ProteinExtractor). This algorithm can combine data from different search algorithms or different experiments (MALDI/ESI, or acquisition repetitions) into a single protein list. Navigation within the database is possible either by using the hierarchy of project, sample, protein/peptide separation, spectrum, and identification results, or by using a gel viewer plug-in. Available features include zooming, annotations (protein, spot name, etc.), export of the annotated image, and links to spot, spectrum, and protein data. Proteinscape includes sophisticated query tools that allow data retrieval for typical questions in proteome projects. Here we present the benefit and power of usage of 6 years of continuous use of the software in over 70 proteome projects managed in house.