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 "chargeStatePredictor false 3 > 2 0.9" > > -Matt > > > On 7/11/2011 11:40 AM, Jimmy Eng wrote: > > 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/W1cQNEEdJvMJ. 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.
