Hi everyone, Has anybody noticed if Xtandem wrongly assigns a charge state of +1 to some peptides which are clearly +2 charged? I'm analyzing Waters data from a QTOF premier, converted using MassWolf 4.2.1 with thresholding of TD 10.0 counts. The Xtandem search was done in TPP v 4.2 rev 1.
The instrument was set to select only +2 and +3 precursors, but I was surprised to see quite a large no. of +1 spectra in the PeptideProphet models, so I decided to track down some of these "+1" peptide sequences, and found that they were assigned +1 in the .tandem file, but in the mzXML file, they were supposed to be +2. If anybody has come across such cases, kindly provide some advice on what may be causing this to happen. Thanks!! Bernt --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
