Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Acknowledgments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
vii
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
PART I SHOTGUN PROTEOMICS OF EXTRACELLULAR
VESICLES AND SUBCELLULAR STRUCTURES
1 Mesenchymal Stem Cell-Derived Extracellular Vesicle
Isolation and Their Protein Cargo Characterization . . . . . . . . . . . . . . . . . . . . . . . . .
3
Miriam Morente-L opez, Juan A. Fafia ´ n-Labora, M onica Carrera,
Francisco J. de Toro, Concha Gil, Jesu ´ s Mateos, and Marı ´a C. Arufe
2 Clinical Proteomics for the Analysis of Circulating Extracellular
Vesicles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Maria N. Barrachina and A ´ ngel Garcı ´a
3 Utilization of Laser Capture Microdissection Coupled to
Mass Spectrometry to Uncover the Proteome of Cellular Protrusions . . . . . . . . . 25
Ana Gordon and Karine Gousset
PART II SHOTGUN PROTEOMICS OF NON-MODEL ORGANISMS
4 Isolation of Apoplastic Fluid from Woody Plant Leaves: Grapevine
and Coffee as a Case Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Andreia Figueiredo and Leonor Guerra-Guimara ˜es
5 Shotgun Proteomics for L3 and L4 Anisakis simplex
Development Stages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Robert Stryin ´ ski, Jesu ´ s Mateos, Elz ˙bieta Łopien ´ ska-Biernat,
and M onica Carrera
6 A Primer and Guidelines for Shotgun Proteomic Analysis
in Non-model Organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Angel P. Diz and Paula Sa ´ nchez-Marı ´n
PART III CLINICAL PROTEOMICS
7 SWATH-MS Protocols in Human Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Maria del Pilar Chantada-Va ´ zquez, Marı ´a Garcı ´a Vence,
Antonio Serna, Cristina Nu ´ n ˜ez, and Susana B. Bravo
8 Serum Proteomic Profiling in Rheumatoid Arthritis
by Antibody Suspension Bead Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Lucı ´a Lourido, Rocı ´o Paz-Gonza ´ lez, Cristina Ruiz-Romero,
Peter Nilsson, and Francisco J. Blanco
ix
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Acknowledgments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
vii
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
PART I SHOTGUN PROTEOMICS OF EXTRACELLULAR
VESICLES AND SUBCELLULAR STRUCTURES
1 Mesenchymal Stem Cell-Derived Extracellular Vesicle
Isolation and Their Protein Cargo Characterization . . . . . . . . . . . . . . . . . . . . . . . . .
3
Miriam Morente-L opez, Juan A. Fafia ´ n-Labora, M onica Carrera,
Francisco J. de Toro, Concha Gil, Jesu ´ s Mateos, and Marı ´a C. Arufe
2 Clinical Proteomics for the Analysis of Circulating Extracellular
Vesicles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Maria N. Barrachina and A ´ ngel Garcı ´a
3 Utilization of Laser Capture Microdissection Coupled to
Mass Spectrometry to Uncover the Proteome of Cellular Protrusions . . . . . . . . . 25
Ana Gordon and Karine Gousset
PART II SHOTGUN PROTEOMICS OF NON-MODEL ORGANISMS
4 Isolation of Apoplastic Fluid from Woody Plant Leaves: Grapevine
and Coffee as a Case Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Andreia Figueiredo and Leonor Guerra-Guimara ˜es
5 Shotgun Proteomics for L3 and L4 Anisakis simplex
Development Stages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Robert Stryin ´ ski, Jesu ´ s Mateos, Elz ˙bieta Łopien ´ ska-Biernat,
and M onica Carrera
6 A Primer and Guidelines for Shotgun Proteomic Analysis
in Non-model Organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Angel P. Diz and Paula Sa ´ nchez-Marı ´n
PART III CLINICAL PROTEOMICS
7 SWATH-MS Protocols in Human Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Maria del Pilar Chantada-Va ´ zquez, Marı ´a Garcı ´a Vence,
Antonio Serna, Cristina Nu ´ n ˜ez, and Susana B. Bravo
8 Serum Proteomic Profiling in Rheumatoid Arthritis
by Antibody Suspension Bead Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Lucı ´a Lourido, Rocı ´o Paz-Gonza ´ lez, Cristina Ruiz-Romero,
Peter Nilsson, and Francisco J. Blanco
ix