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.
