[spctools-discuss] Re: MsFragger vs Comet
Thanks for reply, Alexey. I am using the latest version, and I've posted my question on git.https://github.com/chhh/MSFragger-GUI/issues/63 David On Tuesday, May 22, 2018 at 12:56:51 PM UTC-7, Alexey Nesvizhskii wrote: > > David, > > We have done many comparisons. You should be getting very similar results > when performing closed searches. > You can post questions on MSFragger here: > https://github.com/chhh/MSFragger-GUI/issues > > Also, are you using the latest version? > You can get the latest version of MSFragger here: > http://msfragger.arsci.com/upgrader/ > > Best, > Alexey Nesvizhskii > > On Tuesday, May 22, 2018 at 12:40:51 PM UTC-4, David Zhao wrote: >> >> Hi there, >> >> We've started to evaluate MsFragger tool, has anybody done a comparison >> between Comet and MsFragger? Is it complementary to Comet? We've run a >> couple of MsFragger searches, using parameters converted from comet >> parameters, it seems MsFragger is focusing more on finding more PTMs, which >> results in many long peptide hits, and overriding charge option doesn't >> seem to be working... >> >> Any inputs or comments is greatly appreciated! >> Thanks, >> >> David >> > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] MsFragger vs Comet
Hi there, We've started to evaluate MsFragger tool, has anybody done a comparison between Comet and MsFragger? Is it complementary to Comet? We've run a couple of MsFragger searches, using parameters converted from comet parameters, it seems MsFragger is focusing more on finding more PTMs, which results in many long peptide hits, and overriding charge option doesn't seem to be working... Any inputs or comments is greatly appreciated! Thanks, David -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Export to Spreadsheet function doesn't work
Hi all, The "Export Spreadsheet" button on pepxml viewer doesn't work now, after I click the button, the page is will start to load, but nothing happens in the end. Please help Thanks, David -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: User-defined Modifications library construction and search using SpectraST
Hi Sarah, Thank you for sharing your experience with SpectraST, as regards to the library building, did you use the "lib2html" tool in TPP to display the imported hit in the created library, and check if the hit you wanted are actually in the library? And is there a SpectraST folk here in the group can help us out with user-defined modification library creation and search? Thanks in advance! David On Tuesday, December 15, 2015 at 2:05:53 AM UTC-8, Sarah P. wrote: > > Hi David, > > I'm not able to solve your problem, but I can comfort you, you are not the > only one with these kind of problems. Some months ago, I had similar > problems and until today, I could not really solve them. But in the > meantime, I tried a lot of different things. First, I tried to figure out > where exactly my problem is located. And in some points, it seems to be > similar to yours. So, this is what I did: > > I'm also working with a user defined modification. Searches with comet are > successful, just as in your case. In my case, however, the next step was > kind of a quality control as to the respective modification. So I performed > the TPP workflow to get an interact.ipro.pep.xml. Afterwards, I used the > PepXML Viewer to check on the spectral quality of the modified peptides and > to check whether the TPP assigns the same spectrum to the same modified > sequence than other search engines (comparison of original spectra out of > raw files). So far, it works. > > Just like you, I tried to build the spectral library afterwards by > implementing the modification with the user defined modification file you > described. My file spectrast.usermods looks just like yours, only with a > different mass and a different amino acid residue. When I build the > spectral library with the command line of my computer, I also get a > confirmation of a successful building process. But then, I have problems to > work with the library. Normally, I filter the spectral library for > probability and then review the consensus spectra of the modified peptides > in my spectral library. But in this case, when I build a consensus library > with only high probability spectra, there are no modified peptides anymore, > so I cannot perform any searches of data against the library. So I removed > the probability filter and build up a library. But when I try to evaluate > this spectral library to check on the quality of the modified spectra, to > look at the spectra itself or to check whether the modification is set up > correctly, I have some problems: > > · The same spectra I could look at on the level of ipro.pep.xml > (high probability, correct sequence, correct modification) cannot be found > in the splib anymore. > > · In other cases, I find the same spectra now with very low > probabilities. > > · In a third case, the same spectrum is now displayed as a > spectrum containing another phosphorylation or another sequence (comparison > of scan numbers). > > · Most of my reference spectra will be eliminated as soon as I > filter the spectral library for high probability. > > · Just in case I ignore the differences between PepXML Viewer and > Lorikeet Spectrum Viewer and I look at the peptides displayed in the table > of the splib.html, there are some differences between the table and the > spectrum I see when I click at the peptide in the table. For example, in > your case, in the table, I see the sequence DLK[324]DYFTK. When I click on > the spectrum, it will be displayed with the sequence DLK and without the > modification. > > · To be more precise, the corresponding fragment ion series can’t > be matched or assigned as they don’t belong to the sequence displayed > either in the table or next to the spectrum of the Lorikeet Spectrum > Viewer. The precursor mass of the spectrum, however, belongs to the > sequence of the splib.html-table. The fragment masses, interestingly, are > sometimes even higher than the corresponding precursor masses. > > · My next step will be to find out to which sequence the > displayed fragment ion series could belong, but even if I can figure this > out, I don’t know how this could help. > > · Additionally, when I compare just the raw spectrum (the > spectrum with the same scan number than the spectrum the library took for > the display. I extracted the necessary information directly out of the xml > files.) with the results of other programs, the other softwares will find > another sequence belonging to this raw spectrum. I did not work with a > consensus library when comparing different softwares of course. > > · To complete the view, I just searched for any modified peptides > of the interact.ipro.pep.xml in the spectra of the splib.html, but I found > none. I clicked at every single Lib-ID that corresponds to a modified > peptide and the problem is always the same. > > I repeated these
Re: [spctools-discuss] Possible to run either msconvert or ReAdw on Linux using WINE?
Thanks! On Monday, December 14, 2015 at 10:22:14 AM UTC-8, jsl...@systemsbiology.org wrote: > > http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine > > On Mon, Dec 14, 2015 at 10:16 AM, David Zhao <weizh...@gmail.com > > wrote: > >> Hi there, >> >> Is it possible to run the raw file conversion tool, such as ReAdW or >> msconvert on Linux using WINE or similar? >> Thanks, >> >> David >> >> -- >> 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-discu...@googlegroups.com . >> To post to this group, send email to spctools...@googlegroups.com >> . >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Joe Slagel > Institute for Systems Biology > jsl...@systemsbiology.org > > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Possible to run either msconvert or ReAdw on Linux using WINE?
Hi there, Is it possible to run the raw file conversion tool, such as ReAdW or msconvert on Linux using WINE or similar? Thanks, David -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] Possible to run either msconvert or ReAdw on Linux using WINE?
Will do! I will try to set it up on Linux, though the fact msconvert wine version only worked at one point is a little concerning. David On Monday, December 14, 2015 at 11:34:52 AM UTC-8, Jimmy Eng wrote: > > Report back if you somehow get it to work. I was under the impression > that Visual Studio 2013 has a "garbage" rating with Wine compatibility. A > dev. here compiled msconvert using the VS2010 revision right before the > pwiz project moved over to VS2013 and we can get that running under Wine > but it would be nice to know that current versions run too. > > On Mon, Dec 14, 2015 at 11:03 AM, David Zhao <weizh...@gmail.com > > wrote: > >> Thanks! >> >> On Monday, December 14, 2015 at 10:22:14 AM UTC-8, >> jsl...@systemsbiology.org wrote: >>> >>> http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine >>> >>> On Mon, Dec 14, 2015 at 10:16 AM, David Zhao <weizh...@gmail.com> wrote: >>> >>>> Hi there, >>>> >>>> Is it possible to run the raw file conversion tool, such as ReAdW or >>>> msconvert on Linux using WINE or similar? >>>> Thanks, >>>> >>>> David >>>> >>>> -- >>>> 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-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> Joe Slagel >>> Institute for Systems Biology >>> jsl...@systemsbiology.org >>> >>> -- >> 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-discu...@googlegroups.com . >> To post to this group, send email to spctools...@googlegroups.com >> . >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Tools for ms1 search using mass, retention time and isotopic pattern
Hi there, Is there a tool or tools available for ms1 search using mass, retention time and isotopic pattern like Thermo's pinpoint? This is mainly for Q-exactive data? Thanks in advance! David -- 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. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Sequest search question
Hi there, I have some questions on setting up sequest searches for phospho searches, what's the best way to do this? And do I need to increase max_num_differential_AA_per_mod number accordingly here from 2 to 3 (or 5) in phospho searches? diff_search_options = 43.0 K 16.0 M 0.0 X to diff_search_options = 43.0 K 16.0 M 80.0 STY 0.0 X also is there a way to limit sequest results to just non-terminal modifications for a given residue? Thanks, David -- 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. For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] Is there a sequest equivalent or port that runs from linux and/or written in Java?
Thanks, I will try it out! On Mon, Mar 31, 2014 at 9:59 AM, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Try comet: http://comet-ms.sourceforge.net/ On Mon, Mar 31, 2014 at 9:58 AM, David Zhao weizhao6...@gmail.com wrote: Hi there, I'm wondering if there is a port of sequest algorithm to java available now, or a way to run sequest searches on linux, without having bioworks or discoverer installed. Thanks, David -- 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. For more options, visit https://groups.google.com/d/optout. -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to a topic in the Google Groups spctools-discuss group. To unsubscribe from this topic, visit https://groups.google.com/d/topic/spctools-discuss/UqtZH1SRmRk/unsubscribe . To unsubscribe from this group and all its topics, 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. For more options, visit https://groups.google.com/d/optout. -- 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. For more options, visit https://groups.google.com/d/optout.
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
Aha, thanks Matt! Does msconvert have a centroid mode then? Thanks, David On Wed, Jan 30, 2013 at 12:52 PM, Matt Chambers matt.chamber...@gmail.com 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 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
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
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.
[spctools-discuss] How to determine (retrieve) charge information from jrap's Scan object
Hi there, I'm using jrap to parse mzxml file generated from Thermo's raw file. How can I retrieve charge state information from the Scan project? Thanks, David -- 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/-/UIa_G9DomgIJ. 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.
[spctools-discuss] Having trouble parsing latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap
Hi there, I'm having trouble parsing the latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap: for some scans, scan.getMassIntensityList method returns negative float values for m/z and intensities. Has anybody seen this before? I realized that we're using jrap-0.1.jar, just downloaded jrap-3.0.jar, but still getting negative values. Thanks, David -- 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/-/bpZuwduVT9gJ. 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.
