I wanted to provide an update. First, it appears that the export mgf function from within peak view isn't very good and talking to AB folks it seems more like a left over beta function. Second, the AB folks have unanimously confirmed that the mascot.dlll script shouldn't be used in this case (Analyst TF 1.5 with TripleTOF data), and based on the resulting mgfs and mascot results, I agree. Lastly, I was able to join the beta and the converter has the ability to easily generate an mgf which is exactly what proteinpilot then sends to the Mascot server, albeit without any profile data. It also has an option to make an mzML which works great, only takes about 30 minutes, and results in a ~2 GB file.
I am still struggling with how to get this mzML file to mzXML since certain programs (Progenesis LC-MS, VIPER, MAVEN, etc.) take mzXML not mzML. When I convert the mzML file with msconvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. On Feb 22, 5:59 pm, ben <benane...@gmail.com> wrote: > 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.
