Table 1.
Simulated and experimental datasets
| Experimental type | Dataset | No. of conditions | No. of bio. replicates | No. of mod. peptides | No. of mod. features/site | No. of unmod. Features/site | Data availability | Analysis |
|---|---|---|---|---|---|---|---|---|
| Known ground truth | Computer Simulation 1—Label-free | 2/3/4 | 2/3/5/10 | 1000 | 10 | 10 | Github | |
| Computer Simulation 2—Missing and low features | 2/3/4 | 2/3/5/10 | 1000 | 2 | 10 | Github | ||
| Spike-in benchmark—Ubiquitination—Label-free | 4 | 2 | 12,137 | 1.37 | 10.17 | MSV000088971 | RMSV000000669 | |
| Biological experiment | Human—Ubiquitinatio=n—1mix-TMT | 6 | 2 or 1 | 8848 | 1.21 | 11.01 | MSV000088966 | RMSV000000356 |
| Mouse—Phosphorylation—2mix-TMT | 6 | 4 or 3 | 26,433 | 1.67 | 11.61 | MSV000085565 | RMSV000000357 | |
| Human—Ubiquitination—Label-free | 6 | 2 | 10,799 | 1.40 | 1.65 | MSV000078977 | RMSV000000358 | |
“Dataset” is the dataset code name. “No. of bio. replicates” shows the number of biological replicates per condition. Simulations were generated with different numbers of replicates. The designs of two biological experiments were unbalanced with unequal replicates per condition. “No. of mod. features/site” is the number of features (i.e., peptide ions) used to estimate the abundance of a single modification. “No. of unmod. peptides/protein” is the number of peptide ions without modifications that were used to estimate the global protein abundance. “Data availability” is the ID of the MassIVE.quant repository or the GitHub repository. “Analysis” is the ID of the MassIVE.quant reanalysis container, containing analysis code and modeling results. All the experiments were conducted in data-dependent acquisition (DDA) mode.