4.2蛋白质的结构预测和测定方法.pptVIP

Computational Simulations for Mass Spectrometry based identification of Biological Components Introduction to Mass Spectrometry Mass Spectrometry (MS) is an analytical technique that allows to accurately measure masses of biological molecules. Masses of proteins with known sequence can easily be theoretically calculated by adding masses of individual amino acids. Protein identification is performed through comparison between theoretical masses in a database and experimentally measured masses. Organism Identification Problem: Identify an organism in a complex background mixture by mass measurements. Is it possible? What approaches should be used? What accuracy is required? Simulation Preparation Select a set of proteins that can be reliably measured by mass spectrometry (high intensities, have been observed in nature with no expected modifications) Select a suitable background for the simulation, which will be a good representation of complexity in real world mixtures. Sample: Test organism: E. coli 376 E. coli proteins were selected as representative for the organism due to their abundance as detected in two other microbial MS detections. Background organism selection includes 13 organisms and 83777 proteins: A. thaliana, B. anthracis (genes at NCBI predicted by GeneMark), B. fungorium, D. radiodurans, G. metallireducens, N. europaea, P. aeruginosa, R. palutris, S. putrefaciens, S. cerevisiae, Y. pestis CO92, Y. pestis KIM Bottom up approach: The proteins in the representative E. coli set and the proteins in the background set are broken into pieces in silico (e.g. cut at K and R amino acids). Up to 4 missed cleavages are allowed. There are 70,000 unique peptides in the representative set and 125 million unique peptides in the background set. Example: Protein sequence MRIMVRTLRGDRVALDVDGATTTVAQVKGMVMARERIAVAMQRLFFAGRCLDDDHRTLADYGVRHDSVVF LSLRLATDAYQTEMHNVRLMQPETATAKQEMHQQQQQQLHVHVAADDEEKAIKRKPVSRRALRKILSRLQ Example digest: MR IVR TLR GDR VALDVDGATTTV