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 for your LTQ Velos spectra? Since there's no precursor charge in the underlying RAW file, the converters won't make them up. It's not inconceivable to implement charge state guessing rules, like those implemented in Tandem, but I'm not sure this is going to happen for many reasons. On Mon, Jul 11, 2011 at 9:29 AM, Greg Bowersock <[email protected]> wrote: > 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 (ms level = 2). If the > line isn't there, you might want to check the method on LTQ to make sure > that Charge State Screening is enabled for the segment in the dependent scan > settings. > Greg > > On Mon, Jul 11, 2011 at 11:06 AM, Robert <[email protected]> > wrote: >> >> 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 >> charge would be desirable. >> >> Any suggestions, how the charge could be added to mzXML? >> >> Best, Robert >> >> -- >> 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. >> > > -- > 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. > -- 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.
