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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Timed_29Target_1msconvert32.00003.00003.2.dta
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Timed_29Target_146.00003.00003.2.dta
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