Tandem assigns +1 charge state to a +2 precursor

[Bernt]

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