PART VI: Shotgun proteomics data processing and storage

PART I: Shotgun proteomics of extracellular vesicles and subcellular structures

• Mesenchymal stem cell-derived extracellular vesicles isolation and their protein cargo characterisation

  Miriam Morente López, Juan Antonio Fafián Labora, Mónica Carrera Mouriño, Francisco J. de Toro, Concha Gil, Jesús Mateos Martín, María C. Arufe

  págs. 3-12

  

• Clinical proteomics for the analysis of circulating extracellular vesicles

  Maria N. Barrachina, Ángel García

  págs. 13-23

  

• Utilization of laser capture microdissection coupled to mass spectrometry to uncover the proteome of cellular protrusions

  Ana Gordon, Karine Gousset

  págs. 25-45

  

PART II. Shotgun proteomics of non-model organisms

• Isolation of apoplastic fluid from woody plants leaves: Grapevine and coffee as a case study

  Andreia Figueiredo, Leonor Guerra Guimaraes

  págs. 49-57

  

• Shotgun proteomics for l3 and l4 anisakis simplex development stages

  Robert Stryinski, Jesús Mateos Martín, Elzbieta Lopienska Biernat, Mónica Carrera Mouriño

  págs. 59-75

  

• A primer and guidelines for shotgun proteomic analysis in non-model organisms

  Ángel Pérez Diz, Paula Sánchez Marín

  págs. 77-102

  

PART III: Clinical proteomics

• SWATH-MS Protocols in Human Diseases

  Mª Pilar Chantada Vázquez, María García Vence, Antonio Serna, Cristina Núñez, Susana B. Bravo

  págs. 105-141

  

• Serum proteomic profiling in rheumatoid arthritis by antibody suspension bead arrays

  Lucía Lourido Salas, Rocio Paz, Cristina Ruiz Romero, Peter Nilsson, Francisco J. Blanco

  págs. 143-151

  

• Human blood plasma investigation employing 2d uplc-udmse data-independent acquisition proteomics

  Licia C. Silva Costa, Bradley J. Smith, Pamela T. Carlson, Gustavo H.M. F. Souza, Daniel Martins de Souza

  págs. 153-165

  

• Metaproteomics analysis of host-microbiota interfaces

  Sjoerd Van der Post, Liisa Arike

  págs. 167-179

  

• Mass spectrometry-based analysis of mycobacterial single-colony proteome

  John Iradukunda, Tariq Ganief, Jonathan M. Blackburn, Nelson C. Soares

  págs. 181-189

  

• Proteogenomic approach for mycobacterium tuberculosis investigation

  Julia Bespyatykh, Georgij Arapidi, Egor Shitikov

  págs. 191-201

  

PART IV: Food proteomics

• Shotgun proteomics for food microorganism detection

  Ana G. Abril, Ignacio Ortea García, Jorge Barros Velázquez, Tomás G. Villa, María del Pilar Calo Mata

  págs. 205-213

  

• Shotgun proteomics and protein-based bioinformatics for the characterization of food-derived bioactive peptides

  Mónica Carrera Mouriño, Manuel Pazos, Santiago Aubourg Martínez, Jose M. Gallardo

  págs. 215-223

  

PART V: Analysis of postranslational modifications and protein complexes

• FTSC-labeling coupled with 2DE-LC-MS/MS analysis of complex protein mixtures for identification and relative quantification of tissue carbonylome

  Lucía Méndez, Lorena Barros, Silvia Muñoz, Isabel Medina

  págs. 227-246

  

• Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides

  Chia-Feng Tsai, Jeffrey S. SMITH, Dylan S. Eiger, Kendall J. Martin, Tao Liu, Richard D. Smith, Tujin Shi, Sudarshan Rajagopal, Jon M. Jacobs

  págs. 247-257

  

• Rapid shotgun phosphoproteomics analysis

  Mónica Carrera Mouriño, Benito Cañas Montalvo, Daniel López Ferrer

  págs. 259-268

  

• System-wide profiling of protein-complexes via size exclusion chromatography-mass spectrometry (SEC-MS)

  Andrea Fossati, Fabian Frommelt, Federico Ulliana, Claudia Martelli, Matej Vizovisek, Ludovic C. J. Gillet, Collins Ben, Matthias Gstaiger, Ruedi Aebersold

  págs. 269-294

  

• Qualitative and quantitative shotgun proteomics data analysis from data-dependent acquisition mass spectrometry

  Jesse G. Meyer

  págs. 297-308

  

• The jPOST repository as a public data repository for shotgun proteomics

  Yu Watanabe, A. Yoshikawa, Yasushi Ishihama, Shujiro Okuda

  págs. 309-322