| aggregateByAttributes | Aggregate PSMs to Protein Level |
| convertPDFormat | Convert Proteome Discoverer Output to Required Input Format |
| fitQuantInaccuracyModel | Fit a Random Forest Model |
| getAvgScaledErrorOfLog2FC | Get Average Scaled Error of log2FC for PSMs in a Spike-in Dataset |
| getDistMetric | Get Distance Metric |
| getPSMAttributes | Get attributes for PSMs |
| mergeTrainingSets | Merge Training Sets |
| sample.prot.PD | Sample Protein Data from Protein Discoverer |
| sample.PSM.FP | Sample PSM Data from FragPipe |
| sample.PSM.PD | Sample PSM Data from Proteome Discoverer |