Table 1.
Seven SWATH-MS based benchmark pharmacoproteomic datasets collected for the analysis of this study.
| Datasets | PRIDE ID | Sample size and Dataset description | Analysis Chain | Instrument |
|---|---|---|---|---|
| Nat. Biotechnol. | PXD002952 | 3 samples of 65% human, 30% yeast, and 5% E. coli proteins | LOG-MED-??? | TripleTOF 6600 |
| 34:1130-6, 2016 | 3 samples of 65% human, 15% yeast, and 20% E. coli proteins | |||
| Cell Rep. | PXD003278 | 6 siRNA-treated Cal51 cell samples | LOG-QUA-NON | TripleTOF 5600 |
| 20:1229-41, 2017 | 6 PRPF8-depleted Cal51 cell samples | |||
| Cell. | PXD006106 | 10 formaldehyde treated HeLa Kyoto cell samples | LOG-MED-NON | TripleTOF 5600 |
| 169:1105-18, 2017 | 10 formaldehyde untreated HeLa Kyoto cell samples | |||
| Nat Med. | PXD000672 | 18 tumorous kidney tissue biopsies | LOG-QUA-NON | TripleTOF 5600 |
| 21:407-13, 2015 | 18 non-tumorous kidney tissue biopsies | |||
| Sci Rep. | PXD004880 | 18 plasma samples from individuals with Down syndrome | LOG-MED-NON | TripleTOF 5600 |
| 7:14818, 2017 | 18 plasma samples from healthy controls | |||
| Cell Rep. | PXD003972 | 20 wild type mouse samples | LOG-???-??? | TripleTOF 5600 |
| 18:3219-26, 2017 | 20 knock-in mouse samples expressing endogenous GRB2 | |||
| Mol Syst. Biol. | PXD001064 | 72 blood samples of monozygotic twins | ???-RLR-BAK | TripleTOF 5600 |
| 11:786, 2015 | 44 blood samples of dizygotic twins |
All datasets were from PRIDE database (Navarro et al., 2016). Each method in the analysis chain was abbreviated by a three-letter code as demonstrated in Supplementary Table S1, and ??? indicated that the corresponding method was not specified in the corresponding study of the dataset.