David, You are centroiding "-c" with ReAdW and not with msconvert. Remove centroiding in ReAdW or add it to msconvert and then compare results.
On Wed, Jan 30, 2013 at 12:41 PM, David Zhao <weizhao6...@gmail.com> wrote: > Hi Matt and Jimmy, > > I'm processing a Thermo Q-exactive generated raw file, and I see some > discrenpencies in the mzXML ms/ms peak data and dta generated using > mzxml2search tool by using msconvert or ReAdW-4.6.0.exe. > mzXML was generated using standard parameters without any filter. > ReAdW.exe --mzXML -c > msconvert.exe --mzXML --32 > > and I used mzxml2search from TPP to convert mzXML to dta files, please > find attached dta files for scan 3, they are quite different. > > Thanks, > > David > > > On Mon, Jan 21, 2013 at 1:08 PM, Jimmy Eng <jke...@gmail.com> wrote: > > David, > > > > ReAdW requires the corresponding XRawfile2.dll from Thermo's Xcalibur > > software; it currently won't work with the one from MSFileReader. If I > get > > time this week, I can see if I can get it working with MSFileReader. > > > > > > On Mon, Jan 21, 2013 at 12:51 PM, David Zhao <weizhao6...@gmail.com> > wrote: > >> > >> Thanks, Jimmy. Another question (sorry :-): does ReAdW expects > >> Xrawfile2.dll to reside in a particular directory? My PC is 64 bit > Windows 7 > >> machine, I downloaded Msfilereader from Thermo (I don't have Xcalibur > >> installed on my machine), and installed the 32 bit version. Msconvert > works > >> fine. However, even after I run "regsvr32 C:\Program Files > >> (x86)\Thermo\MSFileReader\XRawfile2.dll", ReAdW still gives me an error: > >> Unable to initialize Xcalibur 2.0 interface; falling back to 1.4 > interface > >> Unable to initialize XCalibur 1.4 interface; check installation > >> hint: try running the command "regsvr32 > >> C:\<path_to_Xcalibur_dll>\XRawfile2.dll" > >> unable to interface with Thermo library > >> > >> So first of all, can I use the dll from MSFileReader with ReAdW.exe, if > I > >> can, how should I register it so it'll be found the program. > >> Thanks so much! > >> > >> David > >> > >> On Sun, Jan 20, 2013 at 11:22 AM, Jimmy Eng <jke...@gmail.com> wrote: > >>> > >>> You can find the ReAdW binary I use here: > >>> https://proteomicsresource.washington.edu/tools.php > >>> > >>> There's no huge changes from previous releases. Mainly minor fixes to > >>> support the Q Exactive instrument, remove 0 intensity peaks for file > size, > >>> etc. > >>> > >>> > >>> 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/ ? > >>>>>> 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/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/ > >>>>>>>>> > >>>>>>>>> Possibly look into OpenMS (I honestly have no clue how pertinent > >>>>>>>>> this is): http://open-ms.sourceforge.net/ > >>>>>>>>> > >>>>>>>>> Also 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 <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.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. > >>>>>>>> > >>>>>>>> -- > >>>>>>>> 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 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. > >>>>>>> > >>>>>>> > >>>>>> -- > >>>>>> 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. > >>>>>> 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. > >>>>> > >>>>> > >>>> -- > >>>> 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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