Re: [spctools-discuss] Decoy database issue

2016-10-04 Thread Luis Mendoza
Hello Min, I am not sure why this is not working for you. I just tested this against one of our databases and it ran with no errors. Can you verify that your source database file does not contain non-standard characters? Or if you are able to, email me the database and I can have a look. Cheers,

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread David Shteynberg
PeptideProphet is doing it's job here by telling you that there is no distinct population of correct results in this search. I suspect your search parameters are the problem. This is orbitrap data so the charges should be known, but it seems Tandem only searched 2+ and 3+ for you, this is somewh

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread Ali
It appears that PeptideProphet fails, I am getting this message: using Accurate Mass Bins using PPM mass difference (X! Tandem) (minprob 0) adding Accurate Mass mixture distr init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: nanoelectros

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread Ali
Thanks for your recommendations David. I added decoys to my data base and I am still getting 0 probabilities for all of the hits. I am attaching my X! Tandem search parameters xml, could you please kindly do me a big favor and check it to see if there is anything suspicious there which might ca