Dear List, I ran a dataset through TPP 4.3.1 on a Win7 machine. The mzXML data was searched using X! Tandem and analyzed by Peptide Prophet. Minimum peptide probability of 0.9 was specified in the Peptide Prophet run. This is followed by Inter Prophet and Protein Prophet (minimum peptide probability = 0.9).
I noticed peptides of probability below 0.9 appearing in the output from Protein Prophet. E.g. Peptide A: initial probability = 0.8996 and nsp adjusted probability = 0.8343. I went back to the output files of Inter Prophet and Peptide Prophet and the same peptide shows probability of 0.9005. Has anyone else observed a similar scenario? It appears that Protein Prophet changed the initial probability of this peptide I was looking at. Does anyone know if the Protein Prophet algorithm makes such a change? Many thanks. Cheers Eric -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
