Thanks Jimmy. I may need a updated version of ReAdW. Do you know if I can let ReAdW or msconvet to output raw file header information, such as method used, serial number, processing mode, etc.
David On Wednesday, January 16, 2013 9:43:47 AM UTC-8, Jimmy Eng wrote: > > Yes, that is the standalone project which is now also used in the TPP. > > For converting Thermo raw files to mzXML, consider using msconvert which > is now the default converter in the TPP. > > I happen to still use ReAdW though. That code actually does get update as > needed but it doesn't get built and distributed via the Sashimi SourceForge > project anymore. Feel free to email me offlist if you want an updated > binary. > > There is no one who currently "owns" jrap. Consider taking ownership of > it yourself if you think you can update it. > > > On Wed, Jan 16, 2013 at 8:40 AM, David Zhao <weizh...@gmail.com<javascript:> > > wrote: > >> Thanks, Jimmy. Is this the project you are referring to: >> https://code.google.com/p/mstoolkit/ ? >> Is ReAdW still the de facto tool to use to convert Thermo's raw files to >> mzXML? It hasn't been updated for years, but like you said, mzXML specs >> hasn't changed either. >> >> BTW, is jrap no longer supported? Could you point to the right person if >> it still is. >> Thanks, >> >> David >> >> >> On Wednesday, January 16, 2013 8:08:00 AM UTC-8, Jimmy Eng wrote: >> >>> I believe MzXML2Search currently uses the mzParser code which you can >>> find in MSToolkit. >>> >>> >>> On Tue, Jan 15, 2013 at 10:23 PM, David Zhao <weizh...@gmail.com> wrote: >>> >>>> Thanks Jimmy and Eric. I'll look into other alternatives as suggested. >>>> My problems that we have a lot of codes still rely on jrap to parse mzXML >>>> file, but jrap can't seem to parse mzXML generated by ReAdW from the >>>> latest >>>> Thermo q exactive instrument ( some scans return negative mz and >>>> intensities). >>>> However, mzxml2search from TPP can parse the mzXML just fine, which >>>> makes me think the jrap is out of date. What parser does mzXML2search use >>>> in this case then? >>>> Thanks, >>>> >>>> David >>>> >>>> On Tuesday, January 15, 2013 9:25:41 PM UTC-8, Eric Deutsch wrote: >>>> >>>>> And if you’re in the market for a Java implementation (like JRAP), >>>>> then I’d recommend jmzreader: >>>>> >>>>> http://code.google.com/p/**jmzre**ader/<http://code.google.com/p/jmzreader/> >>>>> >>>>> >>>>> >>>>> Cheers, >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *From:* spctools...@googlegroups.**com [mailto:spctools...@** >>>>> googlegrou**ps.com] *On Behalf Of *Jimmy Eng >>>>> >>>>> *Sent:* Tuesday, January 15, 2013 9:18 PM >>>>> *To:* spctools...@googlegroups.**com >>>>> >>>>> *Subject:* Re: [spctools-discuss] Re: JRAP question >>>>> >>>>> >>>>> >>>>> At this point, you can probably not worry about jrap not being updated >>>>> because the mzXML format isn't really in flux. But if you want to look >>>>> for >>>>> alternatives ... >>>>> >>>>> >>>>> >>>>> Quite a few folks here would tell you to look at ProteoWizard >>>>> http://proteowizard.**sourceforg**e.net/<http://proteowizard.sourceforge.net/> >>>>> >>>>> Possibly look into OpenMS (I honestly have no clue how pertinent this >>>>> is): http://open-ms.sourceforge.**ne**t/<http://open-ms.sourceforge.net/> >>>>> >>>>> Also MSToolkit: >>>>> https://code.google.com/p/**mst**oolkit/<https://code.google.com/p/mstoolkit/> >>>>> >>>>> >>>>> >>>>> Other folks should chime in if there are other parsing libraries out >>>>> there (which I know there are). >>>>> >>>>> >>>>> >>>>> On Tue, Jan 15, 2013 at 7:20 PM, David Zhao <weizh...@gmail.com> >>>>> wrote: >>>>> >>>>> Thanks Jimmy! So it sounds like jrap is not being updated anymore. If >>>>> i'd like to keep up to date with a mzXML parser, which library should I >>>>> follow? >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> >>>>> David >>>>> >>>>> >>>>> >>>>> On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote: >>>>> >>>>> I'm not a jrap user nor do I know what file are associated with what >>>>> versions. But if you are looking for jrap_3.0.jar and >>>>> jakarta-regexp-1.4.jar, you can find them here: http://sashimi.svn.* >>>>> *sourceforg**e.net/viewvc/**sashimi/trunk/**jrap/sax2/<http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/sax2/> >>>>> >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>> To unsubscribe from this group, send email to spctools-discu...@** >>>>> googlegroups**.com. >>>>> >>>>> For more options, visit this group at http://groups.google.com/**group >>>>> **/spctools-discuss?hl=en<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 view this discussion on the web visit https://groups.google.com/d/** >>>> msg/spctools-discuss/-/**fGumFv11IeEJ<https://groups.google.com/d/msg/spctools-discuss/-/fGumFv11IeEJ> >>>> . >>>> >>>> To post to this group, send email to spctools...@googlegroups.**com. >>>> To unsubscribe from this group, send email to spctools-discu...@** >>>> googlegroups.com. >>>> For more options, visit this group at http://groups.google.com/** >>>> group/spctools-discuss?hl=en<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 view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/XUSCMDHbbCUJ. >> >> To post to this group, send email to >> spctools...@googlegroups.com<javascript:> >> . >> To unsubscribe from this group, send email to >> spctools-discu...@googlegroups.com <javascript:>. >> 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. 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