David, We have done many comparisons. You should be getting very similar results when performing closed searches. You can post questions on MSFragger here: https://github.com/chhh/MSFragger-GUI/issues
Also, are you using the latest version? You can get the latest version of MSFragger here: http://msfragger.arsci.com/upgrader/ Best, Alexey Nesvizhskii On Tuesday, May 22, 2018 at 12:40:51 PM UTC-4, David Zhao wrote: > > Hi there, > > We've started to evaluate MsFragger tool, has anybody done a comparison > between Comet and MsFragger? Is it complementary to Comet? We've run a > couple of MsFragger searches, using parameters converted from comet > parameters, it seems MsFragger is focusing more on finding more PTMs, which > results in many long peptide hits, and overriding charge option doesn't > seem to be working... > > Any inputs or comments is greatly appreciated! > Thanks, > > David > -- 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.
