9 Human Blood Plasma Investigation Employing 2D
UPLC-UDMS
E Data-Independent Acquisition Proteomics . . . . . . . . . . . . . . . . . . 153
Licia C. Silva-Costa, Bradley J. Smith, Pamela T. Carlson,
Gustavo H. M. F. Souza, and Daniel Martins-de-Souza
10 Metaproteomics Analysis of Host–Microbiota Interfaces . . . . . . . . . . . . . . . . . . . . . 167
Sjoerd van der Post and Liisa Arike
11 Mass Spectrometry-Based Analysis of Mycobacterial
Single-Colony Proteome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
John Iradukunda, Tariq Ganief, Jonathan M. Blackburn,
and Nelson C. Soares
12 Proteogenomic Approach for Mycobacterium tuberculosis
Investigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Julia Bespyatykh, Georgij Arapidi, and Egor Shitikov
PART IV FOOD PROTEOMICS
13 Shotgun Proteomics for Food Microorganism Detection . . . . . . . . . . . . . . . . . . . . 205
Ana G. Abril, Ignacio Ortea, Jorge Barros-Vela ´ zquez,
Toma ´ s G. Villa, and Pilar Calo-Mata
14 Shotgun Proteomics and Protein-Based Bioinformatics for
the Characterization of Food-Derived Bioactive Peptides . . . . . . . . . . . . . . . . . . . . 215
M onica Carrera, Manuel Pazos, Santiago P. Aubourg,
and Jose ´ M. Gallardo
PART V ANALYSIS OF POSTRANSLATIONAL MODIFICATIONS
AND PROTEIN COMPLEXES
15 FTSC-Labeling Coupled with 2DE-LC–MS/MS Analysis of
Complex Protein Mixtures for Identification and Relative
Quantification of Tissue Carbonylome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Lucı ´a Me ´ndez, Lorena Barros, Silvia Mun ˜oz, and Isabel Medina
16 Mass Spectrometry-Based Proteomics for Analysis of
Hydrophilic Phosphopeptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Chia-Feng Tsai, Jeffrey S. Smith, Dylan S. Eiger, Kendall Martin,
Tao Liu, Richard D. Smith, Tujin Shi, Sudarshan Rajagopal,
and Jon M. Jacobs
17 Rapid Shotgun Phosphoproteomics Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
M onica Carrera, Benito Can ˜as, and Daniel Lopez-Ferrer
18 System-Wide Profiling of Protein Complexes Via Size
Exclusion Chromatography–Mass Spectrometry (SEC–MS). . . . . . . . . . . . . . . . . . 269
Andrea Fossati, Fabian Frommelt, Federico Uliana,
Claudia Martelli, Matej Vizovisek, Ludovic Gillet,
Ben Collins, Matthias Gstaiger, and Ruedi Aebersold
x
Contents
UPLC-UDMS
E Data-Independent Acquisition Proteomics . . . . . . . . . . . . . . . . . . 153
Licia C. Silva-Costa, Bradley J. Smith, Pamela T. Carlson,
Gustavo H. M. F. Souza, and Daniel Martins-de-Souza
10 Metaproteomics Analysis of Host–Microbiota Interfaces . . . . . . . . . . . . . . . . . . . . . 167
Sjoerd van der Post and Liisa Arike
11 Mass Spectrometry-Based Analysis of Mycobacterial
Single-Colony Proteome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
John Iradukunda, Tariq Ganief, Jonathan M. Blackburn,
and Nelson C. Soares
12 Proteogenomic Approach for Mycobacterium tuberculosis
Investigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Julia Bespyatykh, Georgij Arapidi, and Egor Shitikov
PART IV FOOD PROTEOMICS
13 Shotgun Proteomics for Food Microorganism Detection . . . . . . . . . . . . . . . . . . . . 205
Ana G. Abril, Ignacio Ortea, Jorge Barros-Vela ´ zquez,
Toma ´ s G. Villa, and Pilar Calo-Mata
14 Shotgun Proteomics and Protein-Based Bioinformatics for
the Characterization of Food-Derived Bioactive Peptides . . . . . . . . . . . . . . . . . . . . 215
M onica Carrera, Manuel Pazos, Santiago P. Aubourg,
and Jose ´ M. Gallardo
PART V ANALYSIS OF POSTRANSLATIONAL MODIFICATIONS
AND PROTEIN COMPLEXES
15 FTSC-Labeling Coupled with 2DE-LC–MS/MS Analysis of
Complex Protein Mixtures for Identification and Relative
Quantification of Tissue Carbonylome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Lucı ´a Me ´ndez, Lorena Barros, Silvia Mun ˜oz, and Isabel Medina
16 Mass Spectrometry-Based Proteomics for Analysis of
Hydrophilic Phosphopeptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Chia-Feng Tsai, Jeffrey S. Smith, Dylan S. Eiger, Kendall Martin,
Tao Liu, Richard D. Smith, Tujin Shi, Sudarshan Rajagopal,
and Jon M. Jacobs
17 Rapid Shotgun Phosphoproteomics Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
M onica Carrera, Benito Can ˜as, and Daniel Lopez-Ferrer
18 System-Wide Profiling of Protein Complexes Via Size
Exclusion Chromatography–Mass Spectrometry (SEC–MS). . . . . . . . . . . . . . . . . . 269
Andrea Fossati, Fabian Frommelt, Federico Uliana,
Claudia Martelli, Matej Vizovisek, Ludovic Gillet,
Ben Collins, Matthias Gstaiger, and Ruedi Aebersold
x
Contents