06349cam a2200757 i 4500 ocn818866405 OCoLC 20171113085450.0 m o d cr ||||||||||| 121119s2013 enk ob 001 0 eng 2012046813 9781118493779 (ePub) 111849377X (ePub) 9781118493786 (Adobe PDF) 1118493788 (Adobe PDF) 9781118493960 (MobiPocket) 1118493966 (MobiPocket) 9781118494042 (electronic bk.) 1118494040 (electronic bk.) 9781299188266 (MyiLibrary) 1299188265 (MyiLibrary) 9781119964001 (cloth) 1119964008 (cloth) DEBBG BV041907935 DEBSZ 397475918 DEBSZ 449345076 NLGGC 38119776X NZ1 15351004 ZWZ 191455482 (OCoLC)818866405 (OCoLC)827207580 (OCoLC)828494621 (OCoLC)860503552 DLC eng rda pn DLC DG1 N$T YDXCP IDEBK CDX E7B COO NOC UKDOC NLE EBLCP MHW DEBSZ DEBBG OCLCQ S3O pcc MAIN QP551 SCI 007000 bisacsh 572/.636 23 Eidhammer, Ingvar. Computational and statistical methods for protein quantification by mass spectrometry / Ingvar Eidhammer, Harald Barsnes, Geir Egil Eide, Lennart Martens. [electronic resource] Chichester, West Sussex, United Kingdom : John Wiley & Sons Inc., 2013. 1 online resource. text txt rdacontent computer c rdamedia online resource cr rdacarrier Includes bibliographical references and index. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry; Contents; Preface; Terminology; Acknowledgements; 1 Introduction; 1.1 The composition of an organism; 1.1.1 A simple model of an organism; 1.1.2 Composition of cells; 1.2 Homeostasis, physiology, and pathology; 1.3 Protein synthesis; 1.4 Site, sample, state, and environment; 1.5 Abundance and expression -- protein and proteome profiles; 1.5.1 The protein dynamic range; 1.6 The importance of exact specification of sites and states; 1.6.1 Biological features; 1.6.2 Physiological and pathological features. 1.6.3 Input features1.6.4 External features; 1.6.5 Activity features; 1.6.6 The cell cycle; 1.7 Relative and absolute quantification; 1.7.1 Relative quantification; 1.7.2 Absolute quantification; 1.8 In vivo and in vitro experiments; 1.9 Goals for quantitative protein experiments; 1.10 Exercises; 2 Correlations of mRNA and protein abundances; 2.1 Investigating the correlation; 2.2 Codon bias; 2.3 Main results from experiments; 2.4 The ideal case for mRNA-protein comparison; 2.5 Exploring correlation across genes; 2.6 Exploring correlation within one gene; 2.7 Correlation across subsets. 2.8 Comparing mRNA and protein abundances across genes from two situations2.9 Exercises; 2.10 Bibliographic notes; 3 Protein level quantification; 3.1 Two-dimensional gels; 3.1.1 Comparing results from different experiments -- DIGE; 3.2 Protein arrays; 3.2.1 Forward arrays; 3.2.2 Reverse arrays; 3.2.3 Detection of binding molecules; 3.2.4 Analysis of protein array readouts; 3.3 Western blotting; 3.4 ELISA -- Enzyme-Linked Immunosorbent Assay; 3.5 Bibliographic notes; 4 Mass spectrometry and protein identification; 4.1 Mass spectrometry; 4.1.1 Peptide mass fingerprinting (PMF). 4.1.2 MS/MS -- tandem MS4.1.3 Mass spectrometers; 4.2 Isotope composition of peptides; 4.2.1 Predicting the isotope intensity distribution; 4.2.2 Estimating the charge; 4.2.3 Revealing isotope patterns; 4.3 Presenting the intensities -- the spectra; 4.4 Peak intensity calculation; 4.5 Peptide identification by MS/MS spectra; 4.5.1 Spectral comparison; 4.5.2 Sequential comparison; 4.5.3 Scoring; 4.5.4 Statistical significance; 4.6 The protein inference problem; 4.6.1 Determining maximal explanatory sets; 4.6.2 Determining minimal explanatory sets; 4.7 False discovery rate for the identifications. 4.7.1 Constructing the decoy database4.7.2 Separate or composite search; 4.8 Exercises; 4.9 Bibliographic notes; 5 Protein quantification by mass spectrometry; 5.1 Situations, protein, and peptide variants; 5.1.1 Situation; 5.1.2 Protein variants -- peptide variants; 5.2 Replicates; 5.3 Run -- experiment -- project; 5.3.1 LC-MS/MS run; 5.3.2 Quantification run; 5.3.3 Quantification experiment; 5.3.4 Quantification project; 5.3.5 Planning quantification experiments; 5.4 Comparing quantification approaches/methods; 5.4.1 Accuracy; 5.4.2 Precision; 5.4.3 Repeatability and reproducibility. The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, design and analysis of quantitative proteomics experiments. The author's carefully constructed approach allows readers to easily make the transition into the field of quantitative proteomics. Through detailed descriptions of wet-lab methods, computational approaches and statistical tools, this book covers the full scope of a quantitative experim. Print version record and CIP data provided by publisher. Proteomics Statistical methods. Mass spectrometry Data processing. SCIENCE Life Sciences Biochemistry. bisacsh Proteomik. sao Masspektrometri. sao Electronic books. Electronic books. local Barsnes, Harald. Eide, Geir Egil. Martens, Lennart. Print version: Eidhammer, Ingvar. Computational and statistical methods for protein quantification by mass spectrometry. Chichester, West Sussex, United Kingdom : John Wiley & Sons Inc., 2013 9781119964001 (DLC) 2012033614 http://onlinelibrary.wiley.com/book/10.1002/9781118494042 Wiley Online Library ddc BK 206267 206267