Aha, thanks Matt! Does msconvert have a centroid mode then? Thanks, David
On Wed, Jan 30, 2013 at 12:52 PM, Matt Chambers <[email protected]> wrote: > Hi David, > > -c is not a standard parameter. It is a filter that specifies centroiding > instead of profile mode... thus your ReAdW DTA has peaks and your msconvert > DTA has profile data points. But I also suggest that mzxml2search should > have printed a warning (or did you ignore it?) because the mzXML was > annotated to be in profile mode and profile mode DTAs and MGFs are senseless > AFAIK. > > Hope this helps, > -Matt > > > > On 1/30/2013 2:41 PM, David Zhao 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 <[email protected]> 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 <[email protected]> >>> 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 <[email protected]> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>>>> 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 <[email protected]> >>>>>>>>> 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: [email protected] >>>>>>>>>>> [mailto:[email protected]] On Behalf Of Jimmy Eng >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Sent: Tuesday, January 15, 2013 9:18 PM >>>>>>>>>>> To: [email protected] >>>>>>>>>>> >>>>>>>>>>> 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 <[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/ >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> You received this message because you are subscribed to the >>>>>>>>>>> Google >>>>>>>>>>> Groups "spctools-discuss" group. >>>>>>>>>>> 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. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> 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]. >>>>>>>>>> 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. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> 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 >>>>>> [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. >>>>> >>>>> >>>>> >>>> >>> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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