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Data processing handbook for complex biological data sources

Author: Gauri Misra
Publisher: London : Academic Press, 2019.
Edition/Format:   eBook : Document : EnglishView all editions and formats
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Genre/Form: Electronic books
Additional Physical Format: (OCoLC)1053990481
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Gauri Misra
ISBN: 9780128172803 0128172800
OCLC Number: 1091028876
Notes: Includes index.
Description: 1 online resource
Contents: Front Cover; Data Processing Handbook for Complex Biological Data Sources; Copyright Page; Dedication; Contents; List of contributors; Foreword by Jeremy C. Smith; Foreword by M.R.N. Murthy; Foreword by Aatto Laaksonen; Preface; Acknowledgments; 1 Mass spectroscopy; 1.1 Introduction; 1.1.1 Principle; 1.1.2 Instrumentation; 1.1.3 Types of ionization techniques; 1.1.3.1 Electron ionization; 1.1.3.2 Chemical ionization; 1.1.3.3 Fast atom bombardment; 1.1.3.4 Matrix assisted laser desorption ionization; 1.1.3.5 Electrospray ionization; 1.1.3.6 Fragmentation; 1.1.4 Analyzers 1.1.4.1 Time of flight1.1.4.2 Quadrupole; 1.1.4.3 Ion trap analyzer; 1.1.4.4 Fourier transform-ion cyclotron resistance; 1.1.4.5 Orbitrap analyzer; 1.1.4.6 Tandem mass spectrometer; 1.1.5 Detectors; 1.1.5.1 Faraday cup; 1.1.5.2 Electron multipliers; 1.1.5.3 Photomultipliers; 1.1.5.4 Microchannel plate; 1.1.6 Mass interpretation; 1.1.6.1 Types of peaks; 1.1.6.2 Fragmentation rules; 1.1.6.3 Peptide mass fingerprinting; 1.1.6.4 Peptide fragmentation fingerprinting; 1.1.6.5 De novo peptide sequencing; 1.2 Raw data; 1.2.1 NanoLC principle; 1.2.2 Gradient; 1.2.3 Orbitrap technology 1.2.4 Data-dependent acquisition1.3 Data processing; 1.3.1 Trans-proteomic pipeline; 1.3.2 Installation; 1.3.3 Raw file conversion; 1.3.4 Search engine support; 1.3.5 PeptideProphet for corroboration; 1.3.6 Pep3D to view chromatogram; 1.3.7 iProphet for peptide-level corroboration; 1.3.8 XPRESS/ASAP ratio for peptide quantitation; 1.3.9 Protein prophet for protein interpretation and corroboration; 1.4 Protein quantification and identification; 1.4.1 Label-free quantification; 1.4.2 Functional annotation and enrichment analysis; 1.5 Applications of mass spectrometry 1.5.1 Application in proteomics1.5.2 Application in metabolomics; 1.5.3 Application in environment analysis; 1.5.4 Application in pharmacy; 1.5.5 Application in forensic science; 1.5.6 Applications in medical research; 1.6 Conclusion; References; Further Reading; 2 Circular dichroism; 2.1 Introduction; 2.2 Principle; 2.3 Raw data analyses; 2.3.1 Case study 1: to study acid-induced transitions in a protein; 2.3.2 Case study 2: to study pH-induced transitions in a protein; 2.3.3 Case study 3: to study structural transitions in nucleic acids 2.3.4 Case study 4: determination of Tm and other thermodynamic parameters2.4 Miscellaneous examples; 2.5 Conclusion; Acknowledgments; References; 3 Fluorescence spectroscopy; 3.1 Introduction; 3.2 Principle; 3.2.1 Instrumentation; 3.3 Intrinsic fluorescence; 3.3.1 Protein stability studies; 3.3.2 Protein interaction studies; 3.4 Extrinsic fluorescence; 3.5 Fluorescence polarization; 3.6 Fluorescence resonance energy transfer; 3.7 Conclusion; Acknowledgment; References; 4 High-throughput sequencing; 4.1 Introduction; 4.2 High-throughput sequencing raw data
Responsibility: edited by Gauri Misra.

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