Tissue Proteomics (2^nd Ed., 2nd ed. 2018) Methods and Protocols Methods in Molecular Biology Series, Vol. 1788

This book presents a compilation of methods that detail improved protein and peptide sample preparation and identification. Chapters guide readers through methods for depletion of myofibril-associated proteins, peptide sample preparation in urinary proteomics, purification of targeted proteins from native tissues, fractionation strategies for protein analysis, and GeLC-MS as a sample preparation method for sample preparation for proteomics using minimal amount of tissue. 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 practical, Tissue Proteomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

1. Depletion of Myofibril-Associated Proteins Using Selective Protein Extraction as a Tool in Cardiac Proteomics

Achim Treumann, Pawel Palmowski, Wing Chiu Tong, Julie Taggart, Nick Morrice, G. Nicholas Europe-Finner, and Michael J. Taggart

Tara K. Sigdel and Minnie. M. Sarwal

3. HLA Class I and Class II-Induced Intracellular Signaling and Molecular Associations in Primary Human Endothelial Cells

Nicole Valenzuela, Nwe Nwe Soe, Fang Li, Xiaohai Zhang, Yiping Jin, and Elaine F Reed

4. Characterization of Protein Complexes Using Chemical Cross-linking Coupled Electrospray Mass Spectrometry

5. Optimization for Peptide Sample Preparation for Urine Peptidomics

Tara K Sigdel, Carrie D Nicora, Wei-Jun Qian, and Minnie M Sarwal

6. Purification of Target Proteins from Native Tissues: CCT Complex from Bovine Testes and PP2Ac from Porcine Brains

Feng Guo, Nathan Wlodarchak, Patrick Menden, and Yongna Xing

Nathan Salomonis

8. Untargeted Screening of Urinary Peptides Using Off-line Nano-liquid Chromatography – MALDI-TOF/TOF Mass Spectrometry

François-Ludovic Sauvage, Sébastien Passeron, and Pierre Marquet

9. Identifying Clinically Relevant Proteins for Targeted Analysis in the Development of a Multiplexed Proteomic Biomarker Assay

Emily M. Mackay and Oliver F. Bathe

10. In Situ Hybridization and Double Immunohistochemistry for the Detection of VEGF-A mRNA and CD34/Collagen IV Proteins in Renal Transplant Biopsies

Dejan Dobi and Zoltan G. Laszik

11. LC-SRM-based Targeted Quantification of Urinary Protein Biomarkers

Yuqian Gao, Hui Wang, Carrie D. Nicora, Tujin Shi, Richard D. Smith, Tara Sigdel,  Minnie Sarwal, David G. Camp II, and Wei-Jun Qian

12. Fractionation of Soluble Proteins Using DEAE-, SP-, and Phenyl Sepharose Chromatographies for Proteomics

Parhom Towfighi, Jacob Shaw, and Tara Sigdel

13. GeLC-MS: A Sample Preparation Method for Proteomics Analysis of Minimal Amount of Tissue

14. Targeted Proteomics Verification of Breast Cancer Biomarker Candidates

Iva Procházková, Juraj Lenčo, and Pavel Bouchal

15. Combination Strategy of Quantitative Proteomics Uncovers the Related-Proteins of Colorectal Cancer in the Interstitial Fluid of Colonic Tissue from the AOM-DSS Mouse Model

Guixue Hou, Yang Wang, Xiaomin Lou, and Siqi Liu

16. Multiple Reaction Monitoring using Double Isotopologue Peptide Standards for Protein Quantification

Azad Eshghiand Christoph H. Borchers

17. Isobaric Labeling Based LC-MS/MS Strategy for Comprehensive Profiling of Human Pancreatic Tissue Proteome

Chih-Wei Liu and Qibin Zhang

18. MALDI Imaging Mass Spectrometry of N-glycans and Tryptic Peptides from the same Formalin-Fixed, Paraffin-embedded Tissue Section

19. Differential Adipose Tissue Proteomics

Kelly J Shields

20. Quantification of Breast Cancer Protein Biomarkers at Different Expression Levels in Human Tumors

Yi Chen, David Britton,Elizabeth R. Wood,Stephen Brantley, Michelle Fournier, Marek Wloch, Vonetta Williams, Joseph Johnson, Anthony Magliocco, Ian Pike, and John M. Koomen

21. Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially-resolved Tissue Profiling

Paul D. Piehowski, Rui Zhao, Ronald J. Moore, Geremy C. Clair, and Charles Ansong

22. High-throughput Proteomics Analysis of Fresh-frozen Biopsy Tissue Samples using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry

Yi Zhu and  Tiannan Guo

23. Straightforward Protocol for Gel-free Proteomic Analysis of Adipose Tissue

24. MALDI Imaging Combined to Laser Microdissection-based Microproteomics for Protein Identification. Application to Intratumor Heterogeneity Studies

Rémi Longuespée, Deborah Alberts, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, and Edwin De Pauw

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts