Running MSfragger search in TPP 7.0

[Zeyu Wang]

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!

[David Shteynberg]

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

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[Zeyu Wang]

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?

 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