Table 1.
Overview of breast cancer proteomic studies.
| Reference | ProteomeXchange /CPTAC ID | Method used | Survival | Sample n | Protein n | Reason for exclusion | Eligible |
|---|---|---|---|---|---|---|---|
| Tang et al. (2018) | PXD005692 | LC–MS/MS | Available | 65 | 7141 | – | Yes |
| Terunuma et al. (2014) | NA | GC–MS, LC–MS | Available | 67 | NA | No protein data | No |
| Mertins et al. (2016) | S039 (CPTAC) | LC–MS/MS | Available | 105 | 15,369 | Only 13 events | No |
| Huang et al. (2017) | S032 (CPTAC) | LC–MS/MS | Not available | 24 | 12,794 | No survival data | No |
| Waldemarson et al. (2016) | PXD000944 | 2D-DIGE, LC–MS/MS | Available | 38 | 14,000 | Only 38 samples | No |
| Cifani et al. (2015) | PXD000691 | 2D-DIGE, LC–MS/MS | Available | 38 | 3681 | Only 38 samples | No |
| Liu et al. (2014)a | PXD000260 | nLC-MS/MS | Available | 126 | 2052 | – | Yes |
| Liu et al. (2014)b | PXD000260 | nLC-MS/MS | Available | 126 | 2052 | – | Yes |
| TCGA (2012) | NA | RPPA | Available | 348 | 171 | – | Yes |
| Bouchal et al. (2015) | PXD000029 | iTRAQ-2DLC-MS/MS | Not available | 96 | 4405 | No survival data | No |
| Sjöström et al. (2015) | PXD001685 | LC–MS/MS; LC-SRM | Not available | 80 | 778 | No survival data | No |
| De Marchi et al. (2015) | PXD000485 | LC–MS/MS | Available | 112 | 3109 | – | Yes |
| De Marchi et al. (2016) | PXD002381 | LC–MS/MS | Not available | 38 | 3404 | No survival data | No |
| De Marchi et al. (2016) | PXD002381 | LC–MS/MS | Not available | 38 | 4 | No survival data | No |
| Pozniak et al. (2016) | PXD000815 | LC–MS/MS | Not available | 44 | 10,124 | No survival data | No |
| Pedersen et al. (2017) | PXD005544 | TMT-HILIC; LC–MS/MS | Not available | 34 | 4163 | No survival data | No |
| Zagorec et al. (2018) | PXD008012 | Ti(IV)-IMAC; LC–MS/MS | Not available | 34 | 2643 | No survival data | No |
| Tyanova et al. (2016) | PXD002619 | LC–MS/MS | Not available | 40 | 10,135 | No survival data | No |
| Jiang et al. (2015) | PXD002208 | LC–MS/MS | Not available | 53 | 115 | No survival data | No |
| Haukaas et al. (2015) | NA | RPPA | Not available | 191 | 150 | No survival data | No |
| Ternette et al. (2018) | PXD009738 | nUPLC‐MS/MS | Not available | 11 | 6275 | No survival data | No |
| Chen et al. (2018) | PXD007217 | LC–MS/MS | Not available | 10 | 388 | No survival data | No |
| Naba et al. (2017) | PXD005554 | LC–MS/MS | Not available | 4 | 1000 | No survival data | No |
| Gajbhiye et al. (2017) | PXD006441 | iTRAQ-SCX; LC–MS/MS | Not available | 76 | 365 | No survival data | No |
| Chen et al. (2018) | PXD007572 | LC–MS/MS | Not available | 56 | 556 | No survival data | No |
| Chen et al. (2017) | PXD005214 | LC–MS/MS | Not available | 36 | 2413 | No survival data | No |
| Lobo et al. (2017) | PXD003106 | LC/MS–MS | Not available | 40 | 4175 | No survival data | No |
| Braakman et al. (2017) | PXD003632 | nLC/MS–MS | Not available | 38 | 2995 | No survival data | No |
| Muraoka et al. (2013) | PXD000066 | nLC–MS/MS | Not available | 18 | 7092 | No survival data | No |
| Jordan et al. (2016) | PXD003322 | SPS-based MS3 | Not available | 3 | 6349 | No survival data | No |