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 <[email protected]<javascript:> > > 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 me think the jrap is out of date.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/**jmzreader/<http://code.google.com/p/jmzreader/> >>> >>> >>> >>> Cheers, >>> >>> Eric >>> >>> >>> >>> >>> >>> *From:* spctools...@googlegroups.**com [mailto:spctools...@** >>> googlegroups.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.**sourceforge.net/<http://proteowizard.sourceforge.net/> >>> >>> Possibly look into OpenMS (I honestly have no clue how pertinent this >>> is): http://open-ms.sourceforge.**net/<http://open-ms.sourceforge.net/> >>> >>> Also MSToolkit: >>> https://code.google.com/p/**mstoolkit/<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 <[email protected]> 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.** >>> sourceforge.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. >> >> To post to this group, send email to >> [email protected]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <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. 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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
