Hi, We recently upgraded an old version of TPP (Squall v3.3) to v4.3 rev1. We've noticed an increase in the number of high confidence (<1% FDR) peptides and proteins. Digging into the pepXml files we've seen cases where, for example, a peptide previously assigned a probability of < . 5 now scores > .9. Note that the Mascot scores haven't changed
Where can I learn about the differences between versions of the Prophets? Thanks John -- 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.
