Hi David Thank you for your prompt response. I’ll try out your suggestions today and will update you on the results or if I encounter any issues.
Quick question—are there any specific features in the latest version of TPP that make it particularly well-suited for DDA-LFQ analysis on Bruker instruments? Best Shagun On Wednesday, August 14, 2024 at 11:47:31 AM UTC-4 David Shteynberg wrote: > Hello Shagun, > > I was able to run comet and the TPP on these files from the latest TPP > version 7.1.0. After adding two independent deBruijn randomized decoys to > the database using the Petunia Decoy Database tool, my pipeline found > approximately 80 thousand to almost 90 thousand PSMs at 1% spectrum error > rate, per mzML file. These map to about 68 thousand unique peptides at 1% > peptide error rate, after iProphet combining all the files. ProteinProphet > mapped all of these to just over 7000 proteins at 1% protein error rate (or > lower.) > > The biggest issue I found in your comet params file was the was n-terminal > acetylation was specified using MSFragger notation ‘[^’ for the amino acid > (should be ’n’ instead for comet.) Unfortunately this confused the > pipeline and exposed downstream assumptions that broke the analysis. > > I am attaching the comet params file I used to process this data. > > Cheers! > -David > > P.S. Please update your TPP to the latest 7.1.0 to get the latest > features and bug-fixes! > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/18f72351-1385-4ac7-ae61-bfbb450e9b80n%40googlegroups.com.
