Hi Matt, how about for CID spectra? Is there charge prediction available?
-LW
On Monday, July 11, 2011 9:51:31 AM UTC-7, matt.chambers wrote:
The chargeStatePredictor filter in msconvert will do the standard
single/multiple guessing or ETDZ
prediction for ETD MSn spectra. I.e. --filter
Hi,
when converting Thermo (LTQ velos) raw files to mzXML, no precursor
charges are included in the resulting mzXML. I tried ReAdW (TPP) and
msconvert (Proteowizzard).
This is not a problem for X!Tandem searches, but for some uses
(calculation of mass errors, PRIDE XML repository), the precursor
Precursor charge is already in mzXML. If you look at the mzXML files created
by ReAdW (msconvert should also have it), you should see lines such as:
precursorMz precursorIntensity=2123.5 precursorCharge=4
activationMethod=CID 1390.82/precursorMz
Those lines are part of the msms scan information
Greg, the precursorCharge attribute is only present for data where the
charge state is present in the raw file. This usually is true for
FT/Orbi data but not normally with LTQ/Velos data.
Robert, the real question is what precursor charge would you want to
be associated with each ms/ms spectrum
