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Mass Spectrometry Data Analysis in Proteomics

  • Book
  • © 2020

Overview

Editors:
  1. Rune Matthiesen

    1. Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2051)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Introduction to Mass Spectrometry-Based Proteomics

    • Rune Matthiesen, Jakob Bunkenborg
    Pages 1-58

  3. LC-MS Spectra Processing

    • Rune Matthiesen
    Pages 59-77

  4. Isotopic Distributions

    • Alan L. Rockwood, Magnus Palmblad
    Pages 79-114

  5. Retention Time Prediction and Protein Identification

    • Alex Henneman, Magnus Palmblad
    Pages 115-132

  6. Comparing Peptide Spectra Matches Across Search Engines

    • Rune Matthiesen, Gorka Prieto, Hans Christian Beck
    Pages 133-143

  7. Calculation of False Discovery Rate for Peptide and Protein Identification

    • Gorka Prieto, Jesús Vázquez
    Pages 145-159

  8. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

    • Rune Matthiesen, Ana Sofia Carvalho
    Pages 161-197

  9. Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides

    • Jakob Bunkenborg, Rune Matthiesen
    Pages 199-230

  10. Solution to Dark Matter Identified by Mass-Tolerant Database Search

    • Rune Matthiesen
    Pages 231-240

  11. Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies

    • Barnali Deb, Irene A. George, Jyoti Sharma, Prashant Kumar
    Pages 241-264

  12. Mass Spectrometry-Based Characterization of Ub- and UbL-Modified Proteins

    • Nagore Elu, Benoit Lectez, Juanma Ramirez, Nerea Osinalde, Ugo Mayor
    Pages 265-276

  13. Targeted Proteomics as a Tool for Quantifying Urine-Based Biomarkers

    • Sonali V. Mohan, D. S. Nayakanti, Gajanan Sathe, Irene A. George, Harsha Gowda, Prashant Kumar
    Pages 277-295

  14. Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets

    • Nicolai Bjødstrup Palstrøm, Rune Matthiesen, Hans Christian Beck
    Pages 297-308

  15. Clustering Clinical Data in R

    • Ana Pina, Maria Paula Macedo, Roberto Henriques
    Pages 309-343

  16. Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics

    • Mathias Walzer, Juan Antonio Vizcaíno
    Pages 345-371

  17. Review of Batch Effects Prevention, Diagnostics, and Correction Approaches

    • Jelena Čuklina, Patrick G. A. Pedrioli, Ruedi Aebersold
    Pages 373-387

  18. Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis

    • Yassene Mohammed, Magnus Palmblad
    Pages 389-405

  19. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data

    • Michael J. Eggertson, Keith Fadgen, John R. Engen, Thomas E. Wales
    Pages 407-435

  20. Back Matter

    Pages 437-445
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Keywords

About this book

The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. In contrast to the previous editions, this third edition aims to provide the most relevant computational methods, focusing on computational concepts. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Mass Spectrometry Data Analysis in Proteomics, Third Edition to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal

    Rune Matthiesen

Bibliographic Information

  • Book Title: Mass Spectrometry Data Analysis in Proteomics

  • Editors: Rune Matthiesen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9744-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-4939-9743-5Published: 26 September 2019

  • Softcover ISBN: 978-1-4939-9746-6Published: 26 September 2020

  • eBook ISBN: 978-1-4939-9744-2Published: 24 September 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: X, 445

  • Number of Illustrations: 42 b/w illustrations, 94 illustrations in colour

  • Topics: Mass Spectrometry, Proteomics

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