Table 1. Experimental Data Sets in this Manuscripta.
| Experimental
Design |
Data Availability | ||||
|---|---|---|---|---|---|
| Data Set | Type | No. of Conditions | No. of Bio. Replicates | No. of Tech. Replicates | (MassIVE.quant or R Package) |
| 1: Controlled Mixture–DDA–MaxQuant9 | Group | 4 | 1 | 3 | RMSV000000249.2 |
| 2: Controlled Mixture–DIA–Spectronaut34 | Group | 2 | 1 | 3 | RMSV000000250.2 |
| 3: Controlled Mixture–DDA–Skyline35 | Group | 5 | 1 | 3 | RMSV000000261.1 |
| 4: Mouse–DDA–MaxQuant36 | Paired | 2 | 6 | 2 | RMSV000000292.1 |
| 5: S. cerevisiae–DIA–Skyline37 | Time course | 6 | 3 | 1 | RMSV000000251.1 |
a
“Data Set” is the code name of the data set. “Type” is the type of experimental design (group comparison, paired, or time course. “No. of Conditions” states the number of conditions in the data set. “No. of Bio. Replicates” states the number of biological replicates per condition. “No. of Tech. Replicates” states the number of technical replicates per biological replicate. More details about experimental design and data processing steps for each data sets are available in next section, as listed in “Details in” column. The details of the experimental design, the raw data, the reports, the analysis scripts, the intermediate data processing output files including quantification, testing results are available in MassIVE.quant.