When a precursor charge is not known, the logic that is used to analyze the data is as follows. If there are no peaks above the precursor m/z then the spectrum is assumed to be 1+ and analyzed as such. If there are peaks above the precursor m/z then the precursor ion is assumed to be multiply charged. At this point, although the precursor charge state could be 2+, 3+, 4+ or higher, it is searched as 2+ and 3+.
Note that only correctly presumed charge states can result in 'right' identifications (obviously). This also means that there are likely some 4+ and higher precursor ions that are identified 'wrong' because that precursor charge is never analyzed. It's all a tradeoff (in analysis complexity , search times) and for tryptic peptides it's a generally reasonable one. On Thu, Apr 1, 2010 at 4:41 PM, yinyin li <liyinyin1...@gmail.com> wrote: > Hello: > I collected some data from LTQ XP and converted them to mzXML by ReAdw. > I noticed there is no precursor charge information, unlike the data from LTQ > Orbitrap. > Nevertheless, it seems X!tandem can still get it right. So i become very > curious how it handles the charge. > Does anyone know? > Thanks! > best > yinyin > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
