Proteome Discoverer结果中，这些名词的含义是什么：PSM？FPR？FDR？p-value？PEP？q-value？

Terminology

• PSM: peptide-spectrum match, a spectrum that matches to a peptide sequence
• p-value: probability of observing an incorrect PSM with a given score or higher by chance, low p-value indicates a small probability of observing an incorrect PSM
• FPR: false positive rate, proportion of incorrect PSMs above a certain score threshold over all incorrect PSMs
• FDR: false discovery rate, expected proportion of incorrect predictions amongst a selected set of predictions. The fraction of incorrect PSMs within a selected set of PSMs above a given score threshold.
• q-value: the minimal FDR threshold at which a PSM is accepted, transforming the FDR into a monotone function, increasing the score threshold will always lower the FDR and vice versa
• PEP: posterior error probability (also called local FDR). Measures the significance of a single spectrum assignment with a specific PSM score. It is the probability of the PSM being incorrect, i.e. PEP of 0.01 means there is a 1% chance of the PSM being incorrect.