Main description:

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.

Contents:

1. 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, and Christoph
H. Borchers

2. Quantitative
Analysis of the Wirt5-Regulated Lysine Succinylation Proteome in Mammalian
Cells
Yue Chen

3. Determining
the Composition and Stability of Protein Complexes Using an Integrated Label-Free
and Stable Isotope Labeling Strategy
Todd M. Greco, Amanda J. Guise, and Ileana M. Cristea

4.
Label-Free
Quantitation for Clinical Proteomics
Robert Moulder, Young Ah Goo, and David
R. Goodlett

5. Proteogenomic
Methods to Improve Genome Annotation
Keshava K. Datta, Anil K. Madugundu, and Harsha Gowda

6. Mass
Spectrometry-Based Quantitative O-GlcNAcomic Analysis
Junfeng Ma and Gerald W. Hart

7.
Isolating and
Quantifying Plasma HDL Proteins by Sequential Density Gradient
Ultracentrifugation and Targeted Proteomics
Clark M. Henderson, Tomas Vaisar, and
Andrew N. Hoofnagle

8.
A Method for
Label-Free Differential Top-Down Proteomics
Ioanna Ntai, Timothy K. Toby, Richard
D. LeDuc, and Neil L. Kelleher

9. Multiplexed Immunoaffinity Enrichment of
Peptides with Anti-Peptide Antibodies and Quantification by Stable Isotope
Dilution Multiple Reaction Monitoring Mass Spectrometry
Eric
Kuhn and Steven A. Carr

10. High
Throughput Quantitative Proteomics Enabled by Mass Defect-Based 12-Plex DiLeu
Isobaric Tags
Dustin C. Frost and Lingjun Li

11. Isotopic
N, N-Dimethyl Leucine (iDiLeu) for Absolute Quantification of Peptides Using a
Standard Curve Approach
Tyler Greer and Lingjun Li

12. 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, and Michael J. MacCoss

13. 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, John A. Wrobel,
Jacob Kennedy, DR Mani, Lisa J. Zimmerman, Matthew R. Meyer, Mehdi Mesri, Susan
E. Abbatiello, Emily Boja, Stven A. Carr, Daniel W. Chan, Xian Chen, Jing Chen,
Sherri R. Davies, Matthew J. C. Ellis, David Fenyoe, Tara Hiltke, Karen A.
Ketchum, Chris Kinsinger, Eric Kuhn, Daniel C. Liebler, De Lin, Tao Liu,
Michael Loss, Michael J. MacCoss, Wei-Jun Qian, Robert Rivers, Karin D.
Rodland, Kelly V. Ruggles, Mitchell G. Scott, Richard D. Smith, Stefani Thomas,
R. Reid Townsend, Gordon Whiteley, Chaochao Wu, Hui Zhang, Zhen Zhang, Henry
Rodriguez, and Amanda G. Paulovich

14. Large-Scale
and Deep Quantitative Proteome Profiling Using Isobaric Lableing Coupled with
Two-Dimensional LC-MS/MS
Marina A. Gritsenko, Zhe Xu, Tao Liu,
and Richard D. Smith

15. Multiple
and Selective Reaction Monitoring Using Triple Quadrupole Mass Spectrometer:
Pre-Clinical Large Cohort Analysis
Qin Fu, Zhaohui Chen, Shenyan Zhang,
Sarah Parker, Zongming Fu, Xiaoqian Liu,
Josef Coresh, and Jennifer E. Van Eyk

16. Methods
for SWATH (TM): Data Independent Acquisition on TripleTOF Mass Spectrometers
Ronald J. Holewinski, Sarah J.
Parker, Andrea D. Matlock, Vidya Venkatraman, and Jennifer E. Van Eyk

17. Measurement
of Phosphorylated Peptides with Absolute Quantification
Raven J. Reddy, Timothy G.
Curran, Yi Zhang, and Forest M. White

18.
Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis
Jeffrey N. Savas, Sung Kyu Park, and John
R. Yates III