Liquid chromatography–electrospray ionization tandem
mass spectrometry (LC-ESI MS/MS) .... 206, 211
Liquid chromatography-tandem mass spectrometry
(LC-MS/MS) ......................................5, 8, 10, 11,
15, 18–20, 38, 43, 106, 115–117, 119, 160, 207,
218, 219, 227–245, 248, 259, 262, 263, 298
M
Marine by-product ............................................... 217, 221
Mass spectrometry (MS)...............................5, 10, 25–43,
50, 59, 79, 87, 89, 96, 97, 106, 122, 128, 154,
156, 157, 168, 169, 173, 174, 176, 177, 195,
205–207, 211, 212, 216, 239, 247, 251,
269–293, 297–307, 309, 315
Mesenchymal stem cells (MSCs).................................. 3, 5
Metaproteomics ..................................168, 169, 171, 173
Microbiota ............................................................ 167–178
Microorganism detection .................................... 205–212
Mucus ......................................... 167, 169–171, 174, 177
Multifactorial disorders............................... 153, 154, 156
Mycobacteria ................................................................. 195
O
Oxidative stress.............................................................. 228
P
Pathway analysis ........................................................8, 161
Peptide biomarker......................................................... 211
Phosphopeptide enrichment .............................. 248, 251,
253, 256, 259, 261, 263
Phosphoproteomics ............................ 247–249, 259–267
Platelets............................................................... 16, 17, 21
Pooling samples............................................................... 83
Protein-based bioinformatics .............................. 215–221
Protein co-elution profiling.......................................... 286
Protein complex analysis...................................... 285, 286
Protein extractions .............................4–6, 32, 33, 38, 43,
60, 64, 65, 68, 73, 110–111, 114–120, 135, 171,
183, 208, 211, 212, 230, 240, 259
Proteogenomics ........................... 79, 191, 192, 195, 199
Proteomes........................................ 5, 11, 14, 16, 20, 21,
25–43, 50, 60, 64, 71, 77, 83, 84, 89, 109, 110,
114, 116, 117, 121–124, 131, 133, 156, 168,
169, 174, 178, 181–189, 191, 192, 199, 212,
216, 218–220, 262, 264, 271, 283, 286, 298,
309–311
ProteomeXchange Consortium ................................... 275
Proteomics..........................................3, 8, 11, 13–22, 26,
39, 50, 59–74, 79, 80, 84, 89, 91–93, 99, 107,
115, 116, 118–120, 123, 132, 143–150,
153–164, 177, 181, 182, 192, 195, 205–212,
215–221, 228, 247–256, 270, 275, 279, 297,
298, 300, 309–311
Q
Quantitative proteomics ...................................79, 93, 96,
106, 117, 297, 298
R
Redox proteomics ......................................................... 228
Repositories ..........................................90, 129, 130, 271,
275, 292, 300, 309–321
Rheumatoid arthritis............................................ 143–150
S
Saliva .............................................................110, 114–116
Seafood ................................................................. 217, 221
Serum................................................. 4, 5, 21, 27, 28, 30,
42, 54, 110–112, 114, 115, 118–126, 143, 147,
154, 156–158, 207, 250, 260
Serum/plasma ...................................................... 124, 147
Shotgun proteomics............................. 50, 59, 60, 77–99,
106, 154, 216, 217, 248, 286, 297–306, 309–321
Single-colony ........................................................ 181–188
Strong cation exchange chromatography
(SCX) ..................... 131, 259, 261, 263, 265, 266
SWATH-MS ....................................... 107–110, 113–115,
117, 119, 121, 128–134, 277
T
Tandem mass tags (TMTs) ..................... 59, 60, 248, 310
Tears.....................................................110, 114, 116–117
Titanium dioxide (TiO 2 ) ........... 259–261, 263, 266, 267
TMT labeling ............................... 71, 100, 248–251, 255
Transmission electron microscopy ................................. 18
Tryptic digestion ........................................ 127, 134, 158,
188, 199, 209, 259
2D-DIGE ..................................................................15, 18
2DE....................................................................... 227–245
U
Urine.................................. 110–112, 114, 118, 119, 126
V
VIC method .................................................................... 50
Vitis vinifera .................................................................... 50
324
SHOTGUN PROTEOMICS: METHODS AND PROTOCOLS
Index
mass spectrometry (LC-ESI MS/MS) .... 206, 211
Liquid chromatography-tandem mass spectrometry
(LC-MS/MS) ......................................5, 8, 10, 11,
15, 18–20, 38, 43, 106, 115–117, 119, 160, 207,
218, 219, 227–245, 248, 259, 262, 263, 298
M
Marine by-product ............................................... 217, 221
Mass spectrometry (MS)...............................5, 10, 25–43,
50, 59, 79, 87, 89, 96, 97, 106, 122, 128, 154,
156, 157, 168, 169, 173, 174, 176, 177, 195,
205–207, 211, 212, 216, 239, 247, 251,
269–293, 297–307, 309, 315
Mesenchymal stem cells (MSCs).................................. 3, 5
Metaproteomics ..................................168, 169, 171, 173
Microbiota ............................................................ 167–178
Microorganism detection .................................... 205–212
Mucus ......................................... 167, 169–171, 174, 177
Multifactorial disorders............................... 153, 154, 156
Mycobacteria ................................................................. 195
O
Oxidative stress.............................................................. 228
P
Pathway analysis ........................................................8, 161
Peptide biomarker......................................................... 211
Phosphopeptide enrichment .............................. 248, 251,
253, 256, 259, 261, 263
Phosphoproteomics ............................ 247–249, 259–267
Platelets............................................................... 16, 17, 21
Pooling samples............................................................... 83
Protein-based bioinformatics .............................. 215–221
Protein co-elution profiling.......................................... 286
Protein complex analysis...................................... 285, 286
Protein extractions .............................4–6, 32, 33, 38, 43,
60, 64, 65, 68, 73, 110–111, 114–120, 135, 171,
183, 208, 211, 212, 230, 240, 259
Proteogenomics ........................... 79, 191, 192, 195, 199
Proteomes........................................ 5, 11, 14, 16, 20, 21,
25–43, 50, 60, 64, 71, 77, 83, 84, 89, 109, 110,
114, 116, 117, 121–124, 131, 133, 156, 168,
169, 174, 178, 181–189, 191, 192, 199, 212,
216, 218–220, 262, 264, 271, 283, 286, 298,
309–311
ProteomeXchange Consortium ................................... 275
Proteomics..........................................3, 8, 11, 13–22, 26,
39, 50, 59–74, 79, 80, 84, 89, 91–93, 99, 107,
115, 116, 118–120, 123, 132, 143–150,
153–164, 177, 181, 182, 192, 195, 205–212,
215–221, 228, 247–256, 270, 275, 279, 297,
298, 300, 309–311
Q
Quantitative proteomics ...................................79, 93, 96,
106, 117, 297, 298
R
Redox proteomics ......................................................... 228
Repositories ..........................................90, 129, 130, 271,
275, 292, 300, 309–321
Rheumatoid arthritis............................................ 143–150
S
Saliva .............................................................110, 114–116
Seafood ................................................................. 217, 221
Serum................................................. 4, 5, 21, 27, 28, 30,
42, 54, 110–112, 114, 115, 118–126, 143, 147,
154, 156–158, 207, 250, 260
Serum/plasma ...................................................... 124, 147
Shotgun proteomics............................. 50, 59, 60, 77–99,
106, 154, 216, 217, 248, 286, 297–306, 309–321
Single-colony ........................................................ 181–188
Strong cation exchange chromatography
(SCX) ..................... 131, 259, 261, 263, 265, 266
SWATH-MS ....................................... 107–110, 113–115,
117, 119, 121, 128–134, 277
T
Tandem mass tags (TMTs) ..................... 59, 60, 248, 310
Tears.....................................................110, 114, 116–117
Titanium dioxide (TiO 2 ) ........... 259–261, 263, 266, 267
TMT labeling ............................... 71, 100, 248–251, 255
Transmission electron microscopy ................................. 18
Tryptic digestion ........................................ 127, 134, 158,
188, 199, 209, 259
2D-DIGE ..................................................................15, 18
2DE....................................................................... 227–245
U
Urine.................................. 110–112, 114, 118, 119, 126
V
VIC method .................................................................... 50
Vitis vinifera .................................................................... 50
324
SHOTGUN PROTEOMICS: METHODS AND PROTOCOLS
Index