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Quantitative Proteomics by Mass Spectrometry

  • Book
  • © 2016

Overview

Editors:
  1. Salvatore Sechi

    1. NIDDK, National Institutes of Health, BETHESDA, USA

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  • 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 1410)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards

    • Andrew J. Percy, Juncong Yang, Andrew G. Chambers, Christoph H. Borchers
    Pages 1-21

  3. Quantitative Analysis of the Sirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells

    • Yue Chen
    Pages 23-37

  4. Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy

    • Todd M. Greco, Amanda J. Guise, Ileana M. Cristea
    Pages 39-63

  5. Label-Free Quantitation for Clinical Proteomics

    • Robert Moulder, Young Ah Goo, David R. Goodlett
    Pages 65-76

  6. Proteogenomic Methods to Improve Genome Annotation

    • Keshava K. Datta, Anil K. Madugundu, Harsha Gowda
    Pages 77-89

  7. Mass Spectrometry-Based Quantitative O-GlcNAcomic Analysis

    • Junfeng Ma, Gerald W. Hart
    Pages 91-103

  8. Isolating and Quantifying Plasma HDL Proteins by Sequential Density Gradient Ultracentrifugation and Targeted Proteomics

    • Clark M. Henderson, Tomas Vaisar, Andrew N. Hoofnagle
    Pages 105-120

  9. A Method for Label-Free, Differential Top-Down Proteomics

    • Ioanna Ntai, Timothy K. Toby, Richard D. LeDuc, Neil L. Kelleher
    Pages 121-133

  10. Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry

    • Eric Kuhn, Steven A. Carr
    Pages 135-167

  11. High-Throughput Quantitative Proteomics Enabled by Mass Defect-Based 12-Plex DiLeu Isobaric Tags

    • Dustin C. Frost, Lingjun Li
    Pages 169-194

  12. Isotopic N,N-Dimethyl Leucine (iDiLeu) for Absolute Quantification of Peptides Using a Standard Curve Approach

    • Tyler Greer, Lingjun Li
    Pages 195-206

  13. Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards

    • James G. Bollinger, Andrew B. Stergachis, Richard S. Johnson, Jarrett D. Egertson, Michael J. MacCoss
    Pages 207-221

  14. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

    • Jeffrey R. Whiteaker, Goran N. Halusa, Andrew N. Hoofnagle, Vagisha Sharma, Brendan MacLean, Ping Yan et al.
    Pages 223-236

  15. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC–MS/MS

    • Marina A. Gritsenko, Zhe Xu, Tao Liu, Richard D. Smith
    Pages 237-247

  16. Multiple and Selective Reaction Monitoring Using Triple Quadrupole Mass Spectrometer: Preclinical Large Cohort Analysis

    • Qin Fu, Zhaohui Chen, Shenyan Zhang, Sarah J. Parker, Zongming Fu, Adrienne Tin et al.
    Pages 249-264

  17. Methods for SWATH™: Data Independent Acquisition on TripleTOF Mass Spectrometers

    • Ronald J. Holewinski, Sarah J. Parker, Andrea D. Matlock, Vidya Venkatraman, Jennifer E. Van Eyk
    Pages 265-279

  18. Measurement of Phosphorylated Peptides with Absolute Quantification

    • Raven J. Reddy, Timothy G. Curran, Yi Zhang, Forest M. White
    Pages 281-292

  19. Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis

    • Jeffrey N. Savas, Sung Kyu Park, John R. Yates III
    Pages 293-304

  20. Back Matter

    Pages 305-306
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Keywords

About this book

This volume describes prominent methodologies developed by laboratories that have been leading the field of quantitative proteomics by mass spectrometry. The procedures for performing the experiments are described in an easy-to-understand manner with many technical details that usually are not reported in typical research articles. This second edition of Quantitative Proteomics by Mass Spectrometry provides a broad perspective of the methodologies used for quantifying proteins and post-translational modifications in different types of biomedical specimens. 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 thorough, Quantitative Proteomics by Mass Spectrometry, Second Edition is a valuable resource to help researchers understand and learn about the latest tools used in the study of quantitative proteomics by mass spectrometry.


 

Editors and Affiliations

  • NIDDK, National Institutes of Health, BETHESDA, USA

    Salvatore Sechi

Bibliographic Information

  • Book Title: Quantitative Proteomics by Mass Spectrometry

  • Editors: Salvatore Sechi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3524-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3522-2Published: 12 February 2016

  • Softcover ISBN: 978-1-4939-8066-6Published: 31 March 2018

  • eBook ISBN: 978-1-4939-3524-6Published: 11 February 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIII, 306

  • Number of Illustrations: 37 b/w illustrations, 450 illustrations in colour

  • Topics: Protein Science, Mass Spectrometry

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