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Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Autore Eidhammer Ingvar
Pubbl/distr/stampa Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Descrizione fisica 1 online resource (356 p.)
Disciplina 572.636
572/.636
Altri autori (Persone) BarsnesHarald
EideGeir Egil
MartensLennart
Soggetto topico Proteomics - Statistical methods
Mass spectrometry - Data processing
ISBN 1-118-49404-0
1-299-18826-5
1-118-49378-8
1-118-49377-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto 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
5.4.4 Dynamic range and linear dynamic range
Record Nr. UNINA-9910141482703321
Eidhammer Ingvar  
Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Autore Eidhammer Ingvar
Pubbl/distr/stampa Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Descrizione fisica 1 online resource (356 p.)
Disciplina 572.636
572/.636
Altri autori (Persone) BarsnesHarald
EideGeir Egil
MartensLennart
Soggetto topico Proteomics - Statistical methods
Mass spectrometry - Data processing
ISBN 1-118-49404-0
1-299-18826-5
1-118-49378-8
1-118-49377-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto 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
5.4.4 Dynamic range and linear dynamic range
Record Nr. UNINA-9910831040903321
Eidhammer Ingvar  
Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational and statistical methods for protein quantification by mass spectrometry [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Autore Eidhammer Ingvar
Pubbl/distr/stampa Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Descrizione fisica 1 online resource (356 p.)
Disciplina 572.636
572/.636
Altri autori (Persone) BarsnesHarald
EideGeir Egil
MartensLennart
Soggetto topico Proteomics - Statistical methods
Mass spectrometry - Data processing
ISBN 1-118-49404-0
1-299-18826-5
1-118-49378-8
1-118-49377-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto 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
5.4.4 Dynamic range and linear dynamic range
Record Nr. UNINA-9910841586903321
Eidhammer Ingvar  
Chichester, West Sussex, U.K., : John Wiley & Sons Inc., 2013
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Pubbl/distr/stampa Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Descrizione fisica 1 online resource (298 p.)
Disciplina 572.60285
572/.60285
Altri autori (Persone) EidhammerIngvar
Soggetto topico Proteomics - Data processing
Mass spectrometry - Data processing
Bioinformatics
ISBN 1-281-32178-8
9786611321789
0-470-72430-7
0-470-72429-3
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Protein, proteome, and proteomics -- Protein separation : 2D gel electrophoresis -- Protein digestion -- Peptide separation : HPLC -- Fundamentals of mass spectrometry -- Mass spectrometry : MALDI-TOF -- Protein identification and characterization by MS -- Tandem MS or MS/MS analysis -- Fragmentation models -- Identification and characterization by MS/MS -- Spectral comparisons -- Sequential comparison : de novo sequencing -- Database searching for de novo sequences -- Large-scale proteomics -- Quantitative MS-based proteomics -- Peptides to proteins -- Top-down proteomics -- Standards.
Record Nr. UNINA-9910144576803321
Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Pubbl/distr/stampa Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Descrizione fisica 1 online resource (298 p.)
Disciplina 572.60285
572/.60285
Altri autori (Persone) EidhammerIngvar
Soggetto topico Proteomics - Data processing
Mass spectrometry - Data processing
Bioinformatics
ISBN 1-281-32178-8
9786611321789
0-470-72430-7
0-470-72429-3
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Protein, proteome, and proteomics -- Protein separation : 2D gel electrophoresis -- Protein digestion -- Peptide separation : HPLC -- Fundamentals of mass spectrometry -- Mass spectrometry : MALDI-TOF -- Protein identification and characterization by MS -- Tandem MS or MS/MS analysis -- Fragmentation models -- Identification and characterization by MS/MS -- Spectral comparisons -- Sequential comparison : de novo sequencing -- Database searching for de novo sequences -- Large-scale proteomics -- Quantitative MS-based proteomics -- Peptides to proteins -- Top-down proteomics -- Standards.
Record Nr. UNINA-9910829976803321
Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Computational methods for mass spectrometry proteomics [[electronic resource] /] / Ingvar Eidhammer ... [et al.]
Pubbl/distr/stampa Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Descrizione fisica 1 online resource (298 p.)
Disciplina 572.60285
572/.60285
Altri autori (Persone) EidhammerIngvar
Soggetto topico Proteomics - Data processing
Mass spectrometry - Data processing
Bioinformatics
ISBN 1-281-32178-8
9786611321789
0-470-72430-7
0-470-72429-3
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Protein, proteome, and proteomics -- Protein separation : 2D gel electrophoresis -- Protein digestion -- Peptide separation : HPLC -- Fundamentals of mass spectrometry -- Mass spectrometry : MALDI-TOF -- Protein identification and characterization by MS -- Tandem MS or MS/MS analysis -- Fragmentation models -- Identification and characterization by MS/MS -- Spectral comparisons -- Sequential comparison : de novo sequencing -- Database searching for de novo sequences -- Large-scale proteomics -- Quantitative MS-based proteomics -- Peptides to proteins -- Top-down proteomics -- Standards.
Record Nr. UNINA-9910841561003321
Chichester, England ; ; Hoboken, NJ, : John Wiley & Sons, c2007
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
High-performance algorithms for mass spectrometry-based omics / / Fahad Saeed and Muhammad Haseeb
High-performance algorithms for mass spectrometry-based omics / / Fahad Saeed and Muhammad Haseeb
Autore Saeed Fahad
Pubbl/distr/stampa Cham, Switzerland : , : Springer, , [2022]
Descrizione fisica 1 online resource (146 pages)
Disciplina 005.1
Collana Computational biology
Soggetto topico Computer algorithms
High performance computing
Mass spectrometry - Data processing
ISBN 3-031-01960-1
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Record Nr. UNISA-996490367203316
Saeed Fahad  
Cham, Switzerland : , : Springer, , [2022]
Materiale a stampa
Lo trovi qui: Univ. di Salerno
Opac: Controlla la disponibilità qui
High-performance algorithms for mass spectrometry-based omics / / Fahad Saeed and Muhammad Haseeb
High-performance algorithms for mass spectrometry-based omics / / Fahad Saeed and Muhammad Haseeb
Autore Saeed Fahad
Pubbl/distr/stampa Cham, Switzerland : , : Springer, , [2022]
Descrizione fisica 1 online resource (146 pages)
Disciplina 005.1
Collana Computational biology
Soggetto topico Computer algorithms
High performance computing
Mass spectrometry - Data processing
ISBN 3-031-01960-1
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Record Nr. UNINA-9910591037703321
Saeed Fahad  
Cham, Switzerland : , : Springer, , [2022]
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui