Tissue Proteomics: Methods and Protocols

Front Matter ....Pages i-xii
 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 et al.)....Pages 1-9
 Discovery of Immune Reactive Human Proteins by High-Density Protein Arrays and Customized Validation of Potential Biomarkers by ELISA  (Tara K. Sigdel, Minnie. M. Sarwal)....Pages 11-21
 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, Yi-Ping Jin, Elaine F. Reed)....Pages 23-41
 Characterization of Protein Complexes Using Chemical Cross-Linking Coupled Electrospray Mass Spectrometry  (Timothy D. Cummins, Gopal P. Sapkota)....Pages 43-61
 Optimization for Peptide Sample Preparation for Urine Peptidomics  (Tara K. Sigdel, Carrie D. Nicora, Wei-Jun Qian, Minnie M. Sarwal)....Pages 63-72
 Purification of Target Proteins from Native Tissues: CCT Complex from Bovine Testes and PP2Ac from Porcine Brains  (Feng Guo, Nathan Wlodarchak, Patrick Menden, Yongna Xing)....Pages 73-88
 Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers  (Nathan Salomonis)....Pages 89-111
 Untargeted Screening of Urinary Peptides Using Offline Nano-Liquid Chromatography: MALDI-TOF/TOF Mass Spectrometry  (François-Ludovic Sauvage, Sébastien Passeron, Pierre Marquet)....Pages 113-121
 Identifying Clinically Relevant Proteins for Targeted Analysis in the Development of a Multiplexed Proteomic Biomarker Assay  (Emily M. Mackay, Oliver F. Bathe)....Pages 123-129
 In Situ Hybridization and Double Immunohistochemistry for the Detection of VEGF-A mRNA and CD34/Collagen IV Proteins in Renal Transplant Biopsies  (Dejan Dobi, Zoltan G. Laszik)....Pages 131-143
 LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers  (Yuqian Gao, Hui Wang, Carrie D. Nicora, Tujin Shi, Richard D. Smith, Tara K. Sigdel et al.)....Pages 145-156
 Fractionation of Soluble Proteins Using DEAE-Sepharose, SP-Sepharose, and Phenyl Sepharose Chromatographies for Proteomics  (Parhom Towfighi, Jacob Shaw, Tara Sigdel)....Pages 157-164
 GeLC-MS: A Sample Preparation Method for Proteomics Analysis of Minimal Amount of Tissue  (Manousos Makridakis, Antonia Vlahou)....Pages 165-175
 Targeted Proteomics Driven Verification of Biomarker Candidates Associated with Breast Cancer Aggressiveness  (Iva Procházková, Juraj Lenčo, Pavel Bouchal)....Pages 177-184
 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, Siqi Liu)....Pages 185-192
 Multiple Reaction Monitoring Using Double Isotopologue Peptide Standards for Protein Quantification  (Azad Eshghi, Christoph H. Borchers)....Pages 193-214
 Isobaric Labeling-Based LC-MS/MS Strategy for Comprehensive Profiling of Human Pancreatic Tissue Proteome  (Chih-Wei Liu, Qibin Zhang)....Pages 215-224
 MALDI Imaging Mass Spectrometry of N-glycans and Tryptic Peptides from the Same Formalin-Fixed, Paraffin-Embedded Tissue Section  (Peggi M. Angel, Anand Mehta, Kim Norris-Caneda, Richard R. Drake)....Pages 225-241
 Differential Adipose Tissue Proteomics  (Kelly J. Shields, Changgong Wu)....Pages 243-250
 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 et al.)....Pages 251-268
 Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling  (Paul D. Piehowski, Rui Zhao, Ronald J. Moore, Geremy Clair, Charles Ansong)....Pages 269-277
 High-Throughput Proteomic Analysis of Fresh-Frozen Biopsy Tissue Samples Using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry  (Yi Zhu, Tiannan Guo)....Pages 279-287
 Straightforward Protocol for Gel-Free Proteomic Analysis of Adipose Tissue  (Yvonne Pasing, Armin Schniers, Terkel Hansen)....Pages 289-296
 MALDI Imaging Combined with Laser Microdissection-Based Microproteomics for Protein Identification: Application to Intratumor Heterogeneity Studies  (Rémi Longuespée, Deborah Alberts, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, Edwin De Pauw)....Pages 297-312
Back Matter ....Pages 313-320