Hi David, Thank you for your explanation and suggestions! I will install Java 9 JDK and update the Windows PATH accordingly.
You mentioned several important settings for PeptideProphet in MSFragger searches. Could you help me check if this setting is correct? [image: Snipaste_2024-05-10_21-21-43.png] If I want to perform TMT quantification of peptides with specific PTMs, which modules should I run after the main search? I assume the workflow would be like PeptideProphet -> PTMProphet -> ProteinProphet -> Libra. I'm new to TPP, though I attended your poster session previously. Could you recommend any detailed tutorial resources for using MSFragger in TPP? Thank you! Zeyu Wang On Friday, May 10, 2024 at 6:55:36 PM UTC-4 David Shteynberg wrote: > Hi Zeyu, > > Thanks for your question and for your interest in the TPP. > > Yes I use MSFragger in the TPP and I did run into this exact problem last > week. It required me to install java 9 jdk that I downloaded and installed > from oracle. I then had to make sure that the windows PATH pointed to the > correct version of java from the jdk. Let me know if you cannot find it > and I would be glad to help you further. > > I have found that the PeptideProphet model that seems to function best for > MSFragger searches is the EXPECTSCORE based NONPARAM (semi-supervised) > model, also with the option ONEFVAL to model all the charge states with a > single f-value mixture model. > > Hope you find this useful. > > Cheers! > -David > > On Fri, May 10, 2024 at 3:05 PM Zeyu Wang <[email protected]> wrote: > >> Hi, >> >> Do you use MSFragger in TPP? I downloaded MSFragger 4.0 and renamed it, >> then placed it in this path: C:/TPP/bin/msfragger/msfragger.jar. However, >> when I search my files, it seems to report an error related to the JRE >> version. But MSFragger desktop GUI runs fine: >> >> Error: A JNI error has occurred, please check your installation and try >> again. >> Exception in thread "main" java.lang.UnsupportedClassVersionError: >> edu/umich/andykong/msfragger/MSFragger has been compiled by a more recent >> version of the Java Runtime (class file version 53.0), this version of the >> Java Runtime only recognizes class file versions up to 52.0. >> at java.lang.ClassLoader.defineClass1(Native Method) >> at java.lang.ClassLoader.defineClass(Unknown Source) >> at java.security.SecureClassLoader.defineClass(Unknown Source) >> at java.net.URLClassLoader.defineClass(Unknown Source) >> at java.net.URLClassLoader.access$100(Unknown Source) >> at java.net.URLClassLoader$1.run(Unknown Source) >> 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) >> at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source) >> >> >> Thank you! >> >> -- >> 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 [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/ec3ab6d9-4563-44d8-9e12-65b1f16348d5n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/ec3ab6d9-4563-44d8-9e12-65b1f16348d5n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/048b0740-3d28-4404-ad21-e3c3f5a1fc2cn%40googlegroups.com.
