Hi Elkan, QualScore was specifically written to take PSMs scored by PeptideProphet; more details can be found in the original publication. For search engines that do not have pepXML support, you may have to write a converter to pepXML, or ask the developers of that tool for it. Also of note: since this is open-source software, you also have the option to modify it to take other kinds of input files, scores, etc.
Hope this helps, and good luck! --Luis On Sat, Mar 10, 2012 at 10:28 PM, Naiheng Dong <[email protected]> wrote: > Hi Luis, > > Thanks for your kind reply. > > The command for running QualScore is: java -jar qualscore.jar <options> > <interact-data file> > > So my question is, if I only have .mzXML files, but lose interact-data file, > can I run qualscore to assess the quality of mass spectra in .mzXML file? > > In my opinion, many software such as PepNovo, Crux do not construct > interact-data file, even the .xml files suitable for running PeptideProphet > are not constructed. > > So, what can I do? Do I have to write interact-data file like .xml file by > myself? > > Thanks again. > > Best Regards. > > Elkan > > 在 2012年3月10日 上午7:18，Luis Mendoza <[email protected]>写道： > >> Hello Elkan, >> >> The three columns in that file are: spectrum name, PeptideProphet >> probability, and the quality score, though this file format is only >> produced when you select certain options when you run QualScore. >> >> I am not sure what you mean on your second question. Once you have >> the set of filtered dta files, you can search them with any tool(s) >> you wish (sequence search, de-novo, etc). The TPP also has a utility >> that can create an mzXML file from a directory that contains dta >> files, and you can then use this file for analysis. >> >> Cheers, >> --Luis >> >> >> >> On Fri, Mar 2, 2012 at 8:05 PM, Naiheng Dong <[email protected]> wrote: >> > Hi Luis, >> > >> > Thanks very much for kind help. >> > >> > The Qualscore works very well now. >> > >> > Then another question arised is that, does the third column in the >> > output >> > file .all.qual store the quality scores of each mass spectrum listed in >> > first column? Can we analyze single .dta file without PeptideProphet >> > output >> > files (interact-dataname.pep.xml)? >> > >> > The lectures downloaded about QualScore did not provide any information >> > of >> > the elements listed in qualscore output file. Is there any document >> > written? >> > >> > Thanks again! >> > >> > Best Regards. >> > >> > Elkan >> > >> > >> > 2012/3/2 Luis Mendoza <[email protected]> >> >> >> >> Hello Elkan, >> >> It seems that the current release of TPP contains an incomplete >> >> version of Qualscore. Please go to this link and click on the >> >> 'download' link to get the zip file that contains the software: >> >> >> >> >> >> http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/qualscore_v1.0_2.zip?view=log >> >> >> >> Once you unzip, place the contents (the qualscore.jar file and the >> >> entire lib/ directory) under C:\Inetpub\tpp-bin\ . Make sure you copy >> >> the entire lib/ directory, and not just its contents. >> >> >> >> Hope this helps! >> >> --Luis >> >> >> >> >> >> On Thu, Mar 1, 2012 at 11:00 PM, Naiheng Dong <[email protected]> >> >> wrote: >> >> > Hi Eric >> >> > >> >> > There are two folders in directory C:\Program Files\Java\ (In my >> >> > opinion, >> >> > the lib subdirectory speicfied by you is the lib of Java, and no lib >> >> > folder >> >> > is found in TPP installed directories.), jre1.5.0_03 and jre6. >> >> > >> >> > Under the subdirectory of lib in jre1.5.0_03, the .jar files are: >> >> > deploy.jar, jce.jar, plugin.jar, javaws.jar, jsse.jar, rt.jar, >> >> > with subdirectories: >> >> > images, javaws, applet, classlist, cmm, ext, management, security, >> >> > fonts, >> >> > tzmappings, i386, zi, im. >> >> > >> >> > Under the subdirectory of lib in jre 6, .jar files are: >> >> > charsets.jar, management-agent.jar, deploy.jar, plugin.jar, >> >> > javaws.jar, >> >> > resources.jar, jce.jar, rt.jar, jsse.jar; >> >> > and subfolders are: >> >> > applet, audio, management, classlist, cmm, deploy, ext, security, >> >> > servicetag, fonts, i386, tzmappings, im, zi, images. >> >> > >> >> > None of the .jar files mentioned are found under the subdirectories >> >> > of >> >> > lib >> >> > and the directories under lib. >> >> > >> >> > Thanks very much. >> >> > >> >> > >> >> > 2012/3/2 Eric Deutsch <[email protected]> >> >> >> >> >> >> Hi Elkan, can you describe your situation a little more? Is there a >> >> >> lib >> >> >> directory? What is in it? Are *some* of the jars there, just not >> >> >> all? >> >> >> Or >> >> >> it’s not there at all? >> >> >> >> >> >> >> >> >> >> >> >> Thanks, >> >> >> >> >> >> Eric >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> From: [email protected] >> >> >> [mailto:[email protected]] On Behalf Of Naiheng Dong >> >> >> Sent: Tuesday, February 28, 2012 7:48 PM >> >> >> To: [email protected] >> >> >> Subject: Re: [spctools-discuss] Re: Problem in running QualScore in >> >> >> TPP >> >> >> v4.5.2 >> >> >> >> >> >> >> >> >> >> >> >> Hi Eric >> >> >> >> >> >> Thanks for your reply. >> >> >> >> >> >> All of the .jar files listed by you do not appear in the >> >> >> subdirectory >> >> >> called lib. >> >> >> >> >> >> So how can I repair it? >> >> >> >> >> >> Elkan >> >> >> >> >> >> 在 2012年2月29日 上午11:26，Eric Deutsch >> >> >> <[email protected]>写道： >> >> >> >> >> >> Hi Elkan, I think for QualScore to work, all the supplemental jars >> >> >> like >> >> >> jfreechart-0.9.15.jar need to be in the subdirectory called lib for >> >> >> things >> >> >> to work. So when you execute "java -jar qualscore.jar", it is >> >> >> expecting >> >> >> to >> >> >> find all these files: >> >> >> >> >> >> lib/TableLayout.jar lib/jcommon-0.9.0.jar lib/jfreechart-0.9.15.jar >> >> >> lib/jrap.jar lib/jscicore.jar lib/log4j-1.2.8.jar lib/msutils.jar >> >> >> lib/tar. >> >> >> jar lib/trove.jar lib/xercesImpl.jar >> >> >> >> >> >> Are they there? >> >> >> >> >> >> Eric >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > -----Original Message----- >> >> >> > From: [email protected] [mailto:spctools- >> >> >> > [email protected]] On Behalf Of Jorey Dong >> >> >> > Sent: Tuesday, February 28, 2012 5:18 PM >> >> >> > To: spctools-discuss >> >> >> > Subject: [spctools-discuss] Re: Problem in running QualScore in >> >> >> > TPP >> >> >> > v4.5.2 >> >> >> > >> >> >> > Hi Damian >> >> >> > >> >> >> > Thanks for your kind help. >> >> >> > >> >> >> > When I type the command "java -jar qualscore.jar" in the Windows >> >> >> > command line after moving to directory C:\Inetpub\tpp-bin, error >> >> >> > still >> >> >> > occurs, as listed below: >> >> >> > " >> >> >> > Exception in thread "main" java.lang.NoClassDefFoundError: >> >> >> > org/jfree/ >> >> >> > data/SeriesDataset >> >> >> > Caused by: java.lang.ClassNotFoundException: >> >> >> > org.jfree.data.SeriesDataset >> >> >> > at java.net.URLClassLoader$1.run(Unknown Source) >> >> >> > at java.security.AccessController.doPrivileged(Native >> >> >> > Method) >> >> >> > at java.net.URLClassLoader.findClass(Unknown Source) >> >> >> > at java.lang.ClassLoader.loadClass(Unknown Source) >> >> >> > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown >> >> >> > Source) >> >> >> > at java.lang.ClassLoader.loadClass(Unknown Source) >> >> >> > Could not find the main class: >> >> >> > org.systemsbiology.qualscore.commandline.Main. Program will exit. >> >> >> > " >> >> >> > >> >> >> > Does it mean that the Java Environment I installed is not >> >> >> > appropriate? >> >> >> > >> >> >> > Best Regards. >> >> >> > >> >> >> > Elkan >> >> >> > >> >> >> > On 2月29日, 上午12时33分, GATTACA <[email protected]> wrote: >> >> >> > > Try executing qualscore from the Windows command line: >> >> >> > > cd C:\Inetpub\tpp-bin >> >> >> > > java -jar qualscore.jar >> >> >> > > >> >> >> > > Executing the above commands should give you a usage statement >> >> >> > > for >> >> >> > > Qualscore if everything is okay. >> >> >> > > After that, it's just a question of passing it the write >> >> >> > > parameters. >> >> >> > > >> >> >> > > Damian >> >> >> > > >> >> >> > > On Feb 28, 9:00 am, Jorey Dong <[email protected]> wrote: >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > > Hi All, >> >> >> > > >> >> >> > > > When I run QualScore embedded in TPP to assess the quality of >> >> >> > tandem >> >> >> > > > mass spectra, the error occurs: >> >> >> > > > " >> >> >> > > > run_in c:/Inetpub/wwwroot/ISB/data; java -jar >> >> >> > > > c:\Inetpub\tpp-bin >> >> >> > > > \qualscore.jar -c 1.0 -p 0.1 -a 20060502data06.xml >> >> >> > > >> >> >> > > > java.lang.NoClassDefFoundError: org/jfree/data/SeriesDataset >> >> >> > > > Caused by: java.lang.ClassNotFoundException: >> >> >> > > > org.jfree.data.SeriesDataset >> >> >> > > > at java.net.URLClassLoader$1.run(Unknown Source) >> >> >> > > > at java.security.AccessController.doPrivileged(Native >> >> >> > Method) >> >> >> > > > at java.net.URLClassLoader.findClass(Unknown Source) >> >> >> > > > at java.lang.ClassLoader.loadClass(Unknown Source) >> >> >> > > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown >> >> >> > Source) >> >> >> > > > at java.lang.ClassLoader.loadClass(Unknown Source) >> >> >> > > > Could not find the main class: >> >> >> > > > org.systemsbiology.qualscore.commandline.Main. Program will >> >> >> > > > exit. >> >> >> > > > Exception in thread "main" >> >> >> > > > command "java -jar c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p >> >> >> > > > 0.1 >> >> >> > > > - >> >> >> > a >> >> >> > > > 20060502data06.xml" failed: Operation not permitted >> >> >> > > >> >> >> > > > Command FAILED >> >> >> > > > " >> >> >> > > >> >> >> > > > Same error occurred when I run the data PeptideProphet output >> >> >> > > > file >> >> >> > > > interact-20060502data06.xml. >> >> >> > > >> >> >> > > > So any one can help me solve this problem? >> >> >> > > >> >> >> > > > Best Regards. >> >> >> > > >> >> >> > > > Elkan >> >> >> > >> >> >> > -- >> >> >> > 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 spctools- >> >> >> > [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 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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Naiping Dong (Elkan) >> >> >> >> >> >> -- >> >> >> 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 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. >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Naiping Dong (Elkan) >> >> > >> >> > -- >> >> > 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 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. >> >> >> > >> > >> > >> > -- >> > Naiping Dong (Elkan) >> > >> > -- >> > 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 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. >> > > > > -- > Naiping Dong (Elkan) > > -- > 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 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.
