Hi all! I was wondering what are the command lines required to process with PeptideProphet, iProphet and ProteinProphet the output produced by search engines like comet when run through SearchGUI.
The raw files are in the mgf format and I used a decoy database with the label in the suffix, not the prefix as peptideprophet expects. Everytime I have tried runing this programs I would end up with a 1Kb file containing almost no information. My goal is to link the output of SearchGUI to StPeter, to perform Protein Quantification. I haven't been able to find an in depth guide on how to use these programs, other than the tutorials, which are addressed to people using Petunia, and the help messages of the commands. But no big guide so far on the CLI. Any help would be very much appreciated! Thank you very much for your help! Best regards Antonio -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
