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,
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
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
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
