Table 5. Selected studies of metabolic pathways.
| Topic | Species (specimen) | MS scan | Proteins (peptides) | PTMs | Isotopic labeling (absolute quantification) | Ref. |
|---|---|---|---|---|---|---|
| Acetyl-CoA biosynthesis | Escherichia coli, Saccharomyces cerevisiae | PRM | 177 (901) | None | None | [205] |
| Central carbon metabolism | Bacillus subtilis | SRM | 41 (85) | None | QconCAT | [206] |
| Central carbon metabolism | Corynebacterium glutamicum | SRM | 10 (30) | None | QconCAT (copies/cell) | [207] |
| Central carbon metabolism | Corynebacterium glutamicum | SRM | 19 (57) | None | 15N cells | [208] |
| Central carbon metabolism | Escherichia coli | SRM | 22 (99) | None | PSAQ (pmol/ml cytoplasm) | [209] |
| Central carbon metabolism | Human (colorectal cancer cells, tumors) | PRM, SRM | 75 (208) | None | None, SPPS (pmol/mg protein) | [210] |
| Central carbon metabolism | Human (MCF-7 breast cancer cell line) | SRM | 76 (134) | None | None | [211] |
| Central carbon metabolism | Saccharomyces cerevisiae | SRM | 137 (260) | None | SPPS (copies/cell) | [212] |
| Central carbon, amino acid metabolism | Saccharomyces cerevisiae | SRM | 135 (300) | None | 13C cells | [213] |
| Central carbon, amino acid metabolism | Saccharomyces cerevisiae | SRM | 137 (303) | None | 13C cells | [214] |
| Central carbon, amino acid metabolism | Saccharomyces cerevisiae | SRM | 228 (428) | None | 15N cells | [215] |
| Central carbon, amino acid metabolism | Saccharomyces cerevisiae | SRM | 4 (11) | None, phosphorylation | SPPS (pmol/ml lysate) | [106] |
| Central metabolic pathways | Escherichia coli | SRM | 392 (665) | None | QconCAT (pmol/injection) | [216] |
| Citric acid cycle | Mouse (liver) | SRM | 4 (58) | None | SILAM | [217] |
| Drug metabolism | Human (liver) | SRM | 25 (51) | None | QconCAT (pmol/mg protein) | [218] |
| Drug metabolism | Human (liver) | SRM | 14 (30) | None | SPPS (pmol/mg protein) | [219] |
| Drug metabolism | Human (liver) | SRM | 22 (38) | None | 18O-QconCAT (pmol/mg protein) | [220] |
| Drug metabolism | Human (liver, intestine) | SRM | 13 (13) | None | SPPS (pmol/mg protein) | [221] |
| Drug metabolism | Mouse (6 tissues) | SRM | 27 (27) | None | None, SPPS (pmol/mg protein) | [222] |
| Drug metabolism and transport | Human (intestine, liver, kidney) | PRM, SRM | 43 (44) | None | SPPS (pmol/mg protein) | [223] |
| Drug transport | Human (jejunum, ileum) | SRM | 10 (10) | None | SPPS (pmol/mg protein) | [224] |
| Drug transport | Human (jejunum, ileum) | SRM | 6 (6) | None | QconCAT (pmol/mg protein) | [225] |
| Drug transport | Human (renal cortex) | SRM | 17 (17) | None | SPPS (pmol/mg protein) | [226] |
| Drug transport | Mouse (brain, liver, kidney) | SRM | 36 (38) | None | SPPS (pmol/mg protein) | [227] |
| Eicosanoid synthesis pathway | Mouse (RAW 264.7 macrophage cell line) | SRM | 29 (41) | None | SILAC | [107] |
| Fatty acid synthesis pathway | Escherichia coli | SRM | 12 (22) | None | PSAQ (pmol/ml lysate) | [228] |
| Glycolytic pathway | Human (6 cell lines) | SRM | 24 (80) | None | SIL dimethylation | [229] |
| Glycolytic pathway | Saccharomyces cerevisiae | SRM | 27 (59) | None | QconCAT (copies/cell) | [230] |
| Glycolytic pathway | Saccharomyces cerevisiae | MS1 | 27 (59) | None | QconCAT (copies/cell) | [110] |
| High fat diet metabolic pathways | Mouse (liver) | SRM | 192 (309) | None | SILAC cells, SPPS | [231] |
| Metabolic and photosynthetic | Chlamydomonas reinhardtii | SRM | 88 (105) | None | SPPS (copies/cell) | [108] |
| pathways Mevalonate pathway | Escherichia coli | SRM | 17 (18) | None | QconCAT (pmol/ml cytoplasm) | [232] |
| Mevalonate pathway | Escherichia coli | SRM | 9 (n.i.) | None | None | [104] |
| Mevalonate, tyrosine pathways | Escherichia coli | SRM | 24 (48) | None | None | [102] |
| Mitochondrial metabolism | Human, mouse, rat (liver) | SRM | 57 (118) | None | QconCAT (pmol/mg protein) | [233] |
| Organohalide respiration | Dehalococcoides mccartyi | PRM, SRM | 10 (25) | None | SPPS (copies/cell) | [234] |
| Polyketide pathway | Escherichia coli | SRM | 2 (6) | None | None | [105] |
| Ribosome, glycolytic pathway | Saccharomyces cerevisiae | MS1 | 78 (102) | None | QconCAT (copies/cell) | [147] |
| Terpene pathway | Escherichia coli | SRM | 9 (9) | None | None | [101] |
| Terpene pathway | Picea abies (bark) | SRM | 16 (19) | None | SPPS | [109] |
| Tyr metabolic pathway | Escherichia coli | SRM | 11 (11) | None | None | [103] |
n.i., not indicated