Table 3. Assessment of the validity of proteomics findings based on literature.
| Cell line study (T24M vs. T24) |
# overlapping molecules |
|||
|---|---|---|---|---|
| Category | # molecules | BcCluster | Glad4U | |
| Individual proteomic analysis | Total cell extract | 253 | 19 (7.5%) | 27 (10.7%) |
| ER/Golgi | 217 | 22 (10.1%) | 28 (12.9%) | |
| Conditioned medium | 256 | 27 (10.5%) | 38(14.8%) | |
| Compilation from all proteomics methods | 614 | 54 (8.8%) | 71 (11.6%) | |
| “omics” verified findings | Agreement in all 4 strategies | 11 | 2 (18.2%) | 4 (36.4%) |
| Agreement in 2 or 3 out of 4 strategies | 242 | 31 (12.8%) | 36 (14.9%) | |
| All verified proteins | 253 | 33 (13.0%) | 40 (15.8%) | |
Findings from individual proteomics experiments (CE, ER/Golgi, CM) as well as from the “verified” dataset (established based on statistical significance and expression trend agreement between at least 2 strategies e.g. proteomics analysis of CE, ER/Golgi, CM, and transcriptomics) were evaluated. Proteins extracted from the bladder cancer database (BcCluster)20 and by using GLAD4U21 were utilized as reference.