Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

1. Increased
Depth and Breadth of Plasma Protein Quantitation via Two Dimensional Liquid
Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled
Peptide StandardsAndrew J. Percy, Juncong Yang, Andrew G. Chambers, and Christoph
H. Borchers2. Quantitative
Analysis of the Wirt5-Regulated Lysine Succinylation Proteome in Mammalian
CellsYue Chen3. Determining
the Composition and Stability of Protein Complexes Using an Integrated Label-Free
and Stable Isotope Labeling StrategyTodd M. Greco, Amanda J. Guise, and Ileana M. Cristea4.
Label-Free
Quantitation for Clinical ProteomicsRobert Moulder, Young Ah Goo, and David
R. Goodlett5. Proteogenomic
Methods to Improve Genome AnnotationKeshava K. Datta, Anil K. Madugundu, and Harsha Gowda6. Mass
Spectrometry-Based Quantitative O-GlcNAcomic AnalysisJunfeng Ma and Gerald W. Hart7.
Isolating and
Quantifying Plasma HDL Proteins by Sequential Density Gradient
Ultracentrifugation and Targeted ProteomicsClark M. Henderson, Tomas Vaisar, and
Andrew N. Hoofnagle8.
A Method for
Label-Free Differential Top-Down ProteomicsIoanna Ntai, Timothy K. Toby, Richard
D. LeDuc, and Neil L. Kelleher9. Multiplexed Immunoaffinity Enrichment of
Peptides with Anti-Peptide Antibodies and Quantification by Stable Isotope
Dilution Multiple Reaction Monitoring Mass SpectrometryEric
Kuhn and Steven A. Carr10. High
Throughput Quantitative Proteomics Enabled by Mass Defect-Based 12-Plex DiLeu
Isobaric TagsDustin C. Frost and Lingjun Li11. Isotopic
N, N-Dimethyl Leucine (iDiLeu) for Absolute Quantification of Peptides Using a
Standard Curve ApproachTyler Greer and Lingjun Li12. Selecting
Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as
Analytical StandardsJames G. Bollinger, Andrew B.
Stergachis, Richard S. Johnson, Jarrett D. Egertson, and Michael J. MacCoss13. Using
the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted
Proteomics AssaysJeffrey 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 Fenyö, 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. Paulovich14. Large-Scale
and Deep Quantitative Proteome Profiling Using Isobaric Lableing Coupled with
Two-Dimensional LC-MS/MSMarina A. Gritsenko, Zhe Xu, Tao Liu,
and Richard D. Smith15. Multiple
and Selective Reaction Monitoring Using Triple Quadrupole Mass Spectrometer:
Pre-Clinical Large Cohort AnalysisQin Fu, Zhaohui Chen, Shenyan Zhang,
Sarah Parker, Zongming Fu, Xiaoqian Liu,
Josef Coresh, and Jennifer E. Van Eyk16. Methods
for SWATH¿: Data Independent Acquisition on TripleTOF Mass SpectrometersRonald J. Holewinski, Sarah J.
Parker, Andrea D. Matlock, Vidya Venkatraman, and Jennifer E. Van Eyk17. Measurement
of Phosphorylated Peptides with Absolute QuantificationRaven J. Reddy, Timothy G.
Curran, Yi Zhang, and Forest M. White18.
Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry AnalysisJeffrey N. Savas, Sung Kyu Park, and John
R. Yates III