What does a PEP and PEP Q-value of NaN indicate?

smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

MIT License

90 stars 46 forks source link

What does a PEP and PEP Q-value of NaN indicate? #2415

Closed bluemooninvestor closed 2 weeks ago

bluemooninvestor commented 1 month ago

I am trying to analyze XL-MS data analysis. I have got some interlinks and intralinks at FDR 1%. However, the last 2 columns, PEP and PEP Q-value, read NaN. What does this mean? The Q-value is 0. Sorry, I couldn't find any explainations in the paper.

nbollis commented 1 month ago

A PEP value of NAN indicates that there were not enough peptides to perform Posterior Error Probability. You are currently required to have at least 100 peptides at Q-value<= 0.01