LEADER 05603nam 2200697 a 450 001 9911020318803321 005 20200520144314.0 010 $a9781118494042 010 $a1118494040 010 $a9781299188266 010 $a1299188265 010 $a9781118493786 010 $a1118493788 010 $a9781118493779 010 $a111849377X 035 $a(CKB)2670000000327684 035 $a(EBL)1120718 035 $a(OCoLC)827207580 035 $a(SSID)ssj0000831532 035 $a(PQKBManifestationID)11437142 035 $a(PQKBTitleCode)TC0000831532 035 $a(PQKBWorkID)10873022 035 $a(PQKB)10952289 035 $a(MiAaPQ)EBC1120718 035 $a(DLC) 2012046813 035 $a(PPN)191455482 035 $a(Perlego)1000555 035 $a(EXLCZ)992670000000327684 100 $a20121107d2013 uy 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 10$aComputational and statistical methods for protein quantification by mass spectrometry /$fIngvar Eidhammer ... [et al.] 210 $aChichester, West Sussex, U.K. $cJohn Wiley & Sons Inc.$d2013 215 $a1 online resource (356 p.) 300 $aDescription based upon print version of record. 311 08$a9781119964001 311 08$a1119964008 320 $aIncludes bibliographical references and index. 327 $aComputational 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 327 $a1.6.3 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 327 $a2.8 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) 327 $a4.1.2 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 327 $a4.7.1 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 327 $a5.4.4 Dynamic range and linear dynamic range 330 $a 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 606 $aProteomics$xStatistical methods 606 $aMass spectrometry$xData processing 615 0$aProteomics$xStatistical methods. 615 0$aMass spectrometry$xData processing. 676 $a572/.636 700 $aEidhammer$b Ingvar$01838854 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9911020318803321 996 $aComputational and statistical methods for protein quantification by mass spectrometry$94417940 997 $aUNINA