Hi Luis OK.
Thank you very much for your kind and patient help. Also thank Eric. Best Regards Elkan 在 2012年3月13日 上午6:55，Luis Mendoza <[email protected]>写道： > 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. > > -- 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.
