Online-only Table 1.
List of the public datasets used in this study.
| Dataset name and reference | Original Dataset identifier | Sample types | No of MS/MS spectra | No of unique peptides contributed in the aggregated dataset | Expression Atlas Accession Number (protein expression data) |
|---|---|---|---|---|---|
| Bekker-Jensen_CellSystems_2017 (ref. 17) | PXD004452 | Cell lines, 5 common cell lines | 1.53 E + 07 | 2.54 E + 05 | E-PROT-19 |
| Coscia_NComms_2016 (ref. 12) | PXD003668 | Cell lines, ovarian cancer | 1.03 E + 07 | 1.65 E + 04 | E-PROT-28 |
| Frejno_MolSysBiol_2017 (ref. 13) | PXD005354, PXD005355 | Cell lines, colorectal cancer | 2.14 E + 07 | 1.59 E + 04 | E-PROT-24 |
| Geiger_MCP_2012 (ref. 14) | PXD002395 | Cell lines, 11 common cell lines | 6.38 E + 06 | 5.51 E + 03 | E-PROT-20 |
| Gholami_CellReports_2013 (ref. 15) | PXD005940, PXD005942, PXD005946 | Cell lines, NCI-60 panel | 1.52 E + 07 | 1.12 E + 04 | E-PROT-25 |
| Iglesias-Gato_EurUrology_2016 (ref. 20) | PXD003636, PXD003430, PXD003452, PXD003515, PXD004132, PXD003615, PXD004159 | Tumours, prostate | 1.38 E + 07 | 6.26 E + 03 | E-PROT-21 |
| Lawrence_CellReports_2015 (ref. 10) | PXD008222 | Cell lines, triple-negative breast cancer | 1.95 E + 07 | 4.65 E + 04 | E-PROT-22 |
| Pozniak_CellSystems_2016 (ref. 21) | PXD000815 | Tumours, breast cancer | 3.43 E + 07 | 5.34 E + 03 | E-PROT-26 |
| Tyanova_NComms_2016 (ref. 22) | PXD002619 | Tumours, breast cancer | 1.84 E + 07 | 9.62 E + 03 | E-PROT-27 |
| Wang_Gastroenterology_2017 (ref. 9) | MSV000080374 (MassIVE) | Cell lines, colorectal cancer | 5.50 E + 06 | 1.60 E + 03 | E-PROT-18 |
| Zhang_Nature_2014 (ref. 18) | https://cptac-data-portal.georgetown.edu/cptac/s/S022 | Tumours, colorectal cancer | 1.29 E + 07 | 2.80 E + 03 | E-PROT-23 |