Hopefully the msconvert developers will chime in on whether this info is already or can be exported; this certainly won't happen for ReAdW.
On Sun, Jan 20, 2013 at 8:50 AM, David Zhao <weizhao6...@gmail.com> wrote: > 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> wrote: >> >>> Thanks, Jimmy. Is this the project you are referring to: >>> https://code.google.com/p/**mstoolkit/<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 makes me think the jrap is out of date.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/**jra**p/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/* >>>>> *ms**g/spctools-discuss/-/**fGumFv11I**eEJ<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<https://groups.google.com/d/msg/spctools-discuss/-/XUSCMDHbbCUJ> >>> . >>> >>> 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/-/ZqoIYJSivR0J. > > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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