I didn't realize that about PeakView. So I am generating mgfs from a single wiff 4 ways right now: dll script within Analyst, dll script within Daemon, through PeakView (which took about two seconds), and using Distiller (going on 3 hours right now). Then I will compare them.
Thanks for all the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet <gil...@imsb.biol.ethz.ch> wrote: > Hi Ben, > I do not know how you look at your runs, but the PeakView software (I > use Version 1.1) that open the raw data wiff files can actually export > mgf format. > You need to open the IDA runs with the IDA explorer, select filtering > criteria you want (rt, spectra "quality") and then right click on the > map and export to mgf. You can even get "consensus" spectra during the > mgf export (the software pre-compiles MSMS spectra of close m/z and rt > from parameters you can set yourself). > Hope that helps. > Ludovic > > On Feb 22, 4:17 pm, Matt Chambers <matt.chamber...@gmail.com> wrote: > > > > > > > > > ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can > > msconvert. We're helping to test a new api that will add that support but it > > won't be available until the testing is over (probably another month or so). > > In the meantime, try to get a copy of the AB's new beta standalone converter > > that Eric mentioned. > > > -Matt > > > On Feb 22, 2011 2:55 AM, "Eric Deutsch" <edeut...@systemsbiology.org> wrote: > > > > Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems > > > that the ProteinPilot dll calls that msconvert uses does not get the > > > precursor m/zs right. At least this happened at one time, I'm not certain > > > this is still a problem. However, AB is beta testing a converter tool that > > > will convert a TripleTOF file to an MGF. I don't know about it speed. But > > > you might ask them if you can be a beta tester. > > > > Regards, > > > Eric > > > > > -----Original Message----- > > > > From: spctools-discuss@googlegroups.com [mailto:spctools- > > > > disc...@googlegroups.com] On Behalf Of ben > > > > Sent: Monday, February 21, 2011 11:04 AM > > > > To: spctools-discuss > > > > Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs > > > > > Just wanted to get an idea about what other people get for processing > > > > time when converting wiff files to other formats. Presently I am using > > > > the mascot.dll script within AnalystTF as well as within Mascot Daemon > > > > (the latter taking roughly 4 hours for a single wiff). I am wondering > > > > if using msconvert is the route I should go. Matt seems to recommend > > > > this based on some threads in this group I saw from January, and it > > > > would probably be best to go wiff->mzML->mgf. We could then use either > > > > format to load onto our mascot server. Our goal is to get our raw data > > > > out and be able to analyze it however we want, beyond protein pilot. > > > > > Bottomline: > > > > - It is super slow using a 32-bit machine running XP to convert wiffs > > > > to mgfs with the mascot.dll script. What's my best choice/tool? > > > > - Is the only way to download msconvert with the TPP package? Any > > > > direct download links? > > > > - I can get a version of ProteinPilot3 and install without a lic, or > > > > is Skyline a better alternative? > > > > > Sorry for the remedial questions, but reading through other posts I > > > > figured it might be best to ask before I start. Thanks for any help I > > > > can get. > > > > > - Ben -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@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.
