Re: [spctools-discuss] Re: JRAP question
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
Re: [spctools-discuss] Re: JRAP question
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
Re: [spctools-discuss] Re: JRAP question
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 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
Re: [spctools-discuss] Re: JRAP question
: 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. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [spctools-discuss] Re: JRAP question
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.comjavascript: 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/**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/**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=enhttp://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/-/**fGumFv11IeEJhttps://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=enhttp://groups.google.com/group/spctools-discuss?hl=en . -- You received this message because you are subscribed to the Google Groups spctools-discuss group
Re: [spctools-discuss] Re: JRAP question
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.comwrote: 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 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/**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=enhttp://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**eEJhttps://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
Re: [spctools-discuss] Re: JRAP question
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 weizhao6...@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/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 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/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=enhttp://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-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. 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.
Re: [spctools-discuss] Re: JRAP question
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.comjavascript: 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 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/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=enhttp://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.comjavascript: . To unsubscribe from this group, send email to spctools-discu...@googlegroups.com 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 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.
Re: [spctools-discuss] Re: JRAP question
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 weizhao6...@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/**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/**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=enhttp://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/-/**fGumFv11IeEJhttps://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=enhttp://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-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
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 weizhao6...@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/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-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.
RE: [spctools-discuss] Re: JRAP question
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-discuss@googlegroups.com [mailto: spctools-discuss@googlegroups.com] *On Behalf Of *Jimmy Eng *Sent:* Tuesday, January 15, 2013 9:18 PM *To:* spctools-discuss@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 weizhao6...@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-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. 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.
