INDEX
A
Anisakis simplex.........................................................59–74
Antibody bead arrays ........................................... 143–150
Apoplast ........................................................49–51, 53–56
Apoplastic fluid (APF) ..............................................49–56
B
Bacterial proteome ........................................................ 182
Beijing B0/W148 ......................................................... 192
Bioactive peptides ................................................ 215–222
Biomarker discoveries .......................................... 107, 118
C
Cellular protrusions ..................................................25–44
Coffea arabica ................................................................. 50
Coffee leaves.................................................................... 55
Concentrations ..............................................7, 18, 20–22,
27–29, 31, 32, 38, 42, 50, 51, 53, 55, 66, 69, 70,
73, 74, 84, 89, 96, 99, 114–119, 121–126, 146,
147, 154, 156, 158, 163, 171, 172, 177, 184,
188, 196, 208–210, 219, 235, 236, 239,
241–243, 250, 252, 253, 255, 256, 262, 263,
277, 278, 289
D
Databases .............................................. 11, 15, 16, 19–21,
40, 64, 71, 78, 79, 89–92, 133, 157, 161, 168,
170, 174–176, 178, 185, 191, 192, 198, 199,
207, 210, 211, 216, 218, 220, 221, 255, 264,
277, 283, 287, 298, 300–302, 306, 309, 311,
312, 321
Data-dependent acquisition (DDA) ...................... 10, 98,
106, 108, 129, 131–133, 135, 210, 239, 288,
292, 297–306
Data normalization ......................................................... 94
Depletion .................................................... 114, 118–120,
122, 124, 125, 154, 158, 161
Dimethyl-3-3
0 -dithiobispropiomimidate (DTBP) ....... 27,
28, 32, 40
E
Electrophoresis ..................................................19, 22, 61,
67, 73, 79, 81, 85, 93, 96, 112, 127, 193, 194,
233, 237, 241, 243, 315
Extracellular vesicles (EVs)............................ 3–11, 13–22
F
Fixation .............................. 6, 27, 28, 30, 32, 40, 96, 146
Fluorescein 5-thiosemicarbazide (FTSC) ........... 227–245
Foods ..................................................105, 115, 205–212,
215–217, 219, 221, 230
G
Gene ontology analysis ........................................ 300, 301
Genome ............................................................. 77–79, 92,
191, 192, 199, 298
Grapevine leaves ................................................. 50, 55, 56
H
High-intensity focused ultrasound (HIFU) ................. 60,
61, 259, 261–263
Hydrophilic phosphopeptides ............................. 247–256
I
Immunoaffinity depletion.................................... 154, 155
Interference ....................................................97, 121, 228
Intestine ........................................................168–170, 215
In vivo protein carbonylation ....................................... 228
Isobaric labelling ........................................ 72, 80, 82–83,
88–89, 92, 93
J
Jurkat T-cells ..................... 259, 260, 262, 265–267, 272
L
Label free LC-MS/MS .............................................18, 19
Laser capture microdissection (LCM) .....................25–43
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4, © Springer Science+Business Media, LLC, part of Springer Nature 2021
323
A
Anisakis simplex.........................................................59–74
Antibody bead arrays ........................................... 143–150
Apoplast ........................................................49–51, 53–56
Apoplastic fluid (APF) ..............................................49–56
B
Bacterial proteome ........................................................ 182
Beijing B0/W148 ......................................................... 192
Bioactive peptides ................................................ 215–222
Biomarker discoveries .......................................... 107, 118
C
Cellular protrusions ..................................................25–44
Coffea arabica ................................................................. 50
Coffee leaves.................................................................... 55
Concentrations ..............................................7, 18, 20–22,
27–29, 31, 32, 38, 42, 50, 51, 53, 55, 66, 69, 70,
73, 74, 84, 89, 96, 99, 114–119, 121–126, 146,
147, 154, 156, 158, 163, 171, 172, 177, 184,
188, 196, 208–210, 219, 235, 236, 239,
241–243, 250, 252, 253, 255, 256, 262, 263,
277, 278, 289
D
Databases .............................................. 11, 15, 16, 19–21,
40, 64, 71, 78, 79, 89–92, 133, 157, 161, 168,
170, 174–176, 178, 185, 191, 192, 198, 199,
207, 210, 211, 216, 218, 220, 221, 255, 264,
277, 283, 287, 298, 300–302, 306, 309, 311,
312, 321
Data-dependent acquisition (DDA) ...................... 10, 98,
106, 108, 129, 131–133, 135, 210, 239, 288,
292, 297–306
Data normalization ......................................................... 94
Depletion .................................................... 114, 118–120,
122, 124, 125, 154, 158, 161
Dimethyl-3-3
0 -dithiobispropiomimidate (DTBP) ....... 27,
28, 32, 40
E
Electrophoresis ..................................................19, 22, 61,
67, 73, 79, 81, 85, 93, 96, 112, 127, 193, 194,
233, 237, 241, 243, 315
Extracellular vesicles (EVs)............................ 3–11, 13–22
F
Fixation .............................. 6, 27, 28, 30, 32, 40, 96, 146
Fluorescein 5-thiosemicarbazide (FTSC) ........... 227–245
Foods ..................................................105, 115, 205–212,
215–217, 219, 221, 230
G
Gene ontology analysis ........................................ 300, 301
Genome ............................................................. 77–79, 92,
191, 192, 199, 298
Grapevine leaves ................................................. 50, 55, 56
H
High-intensity focused ultrasound (HIFU) ................. 60,
61, 259, 261–263
Hydrophilic phosphopeptides ............................. 247–256
I
Immunoaffinity depletion.................................... 154, 155
Interference ....................................................97, 121, 228
Intestine ........................................................168–170, 215
In vivo protein carbonylation ....................................... 228
Isobaric labelling ........................................ 72, 80, 82–83,
88–89, 92, 93
J
Jurkat T-cells ..................... 259, 260, 262, 265–267, 272
L
Label free LC-MS/MS .............................................18, 19
Laser capture microdissection (LCM) .....................25–43
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4, © Springer Science+Business Media, LLC, part of Springer Nature 2021
323