Thanks for the thorough explanation. I agree that this logic works quite successfully. At least in my hands, the data from LTQ without charge information work as well as these from orbitrap, in terms of protein ID. best yinyin
On Fri, Apr 2, 2010 at 12:01 PM, Jimmy Eng <jke...@gmail.com> wrote: > 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<spctools-discuss%2bunsubscr...@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<spctools-discuss%2bunsubscr...@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.
