24.1
Proteomics Databases: Navigating the Archipelago
Henning Hermjakob
Swiss-Prot, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Proteomics data is much more diverse than genetic data, important data types include for example, 2D gel images, mass spectra, and protein interactions. For each data type, the publicly available data is often distributed over several databases, journals’ and authors’ websites.
We will give an introduction to navigation in the proteomics data archipelago, zooming in from an overview map of data types, database contents and features to a more detailed exploration of protein-protein interaction databases. We’ll point out treasure troves of high quality data and harbours of friendly user interfaces or what might await you after password-protected walls. In particular, we’ll focus on bridges of interoperability between islands and possibilities of building new bridges of data integration.
24.2
A Tutorial on Systematic Proteomics Analyses
Soeren Schandorff
MDS Proteomics, Odense, Denmark
Technology developments in proteomics make possible systematic large- scale studies of protein interactions, differential expression, post-transla- tional modifications and other pathway related information enabling challenging systems biology approaches. Bioinformatics is a fundamental component in the systems biology approaches for the organizing, analysing and display of these rather complex proteomics data. One additional element to this has been the revealing of the prevalence of alternative splicing which besides giving rise to higher complexity of the proteome also have added a serious complexity aspect to the distinction of information with respect to specific isoforms, which is currently rather poorly handled. This fundamental role of bioinformatic affects our way of thinking about proteomics and bioinformatic decisions partly govern on which terms we can compare different proteomics information and how. How can one be inclusive without drowning in information for which there is no common base for comparison? Starting from current large-scale proteom- ics analyses undertaken at MDS Proteomics and other proteomics companies an introduction will be given to the general concepts and approaches in tightly integrated bioinformatic solutions for the management and analyses of results from systematic proteomics studies.
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Published online: September 01, 2002
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© 2002 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.
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