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Báo cáo sinh học: " Optimal selection of epitopes for TXPimmunoaffinity mass spectrometyr"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Optimal selection of epitopes for TXPimmunoaffinity mass spectrometry. | Planatscher et al. Algorithms for Molecular Biology 2010 5 28 http www.almob.Org content 5 1 28 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry 1 14 2 3 2 2 Hannes Planatscher Jochen Supper 1 Oliver Poetz Dieter Stoll Thomas Joos Markus F Templin Andreas Zell1 Abstract Background Mass spectrometry MS based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes promise a significant gain in efficiency. Results We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties. Conclusions For small datasets a few hundred proteins it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets like full proteomes require the use of heuristics. Background Mass spectrometry MS based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. Contrary to the analysis of mRNA profiles the .