From SPCTools

Using Novor in TPP

About Novor

Novor is a de-novo peptide sequencing engine; academic and industrial licenses are offered.

Current status in TPP

Novor searches can be launched from the interface, including ability to edit the parameters file. The results can be converted to pepXML and visualized in the PepXMLViewer, with links to the interpreted spectra and full capabilities to sort and filter. A graphical representation of the aminoacid scores is also shown in this viewer.

Plans for deeper integration into the rest of the pipeline are underway.

Launching

One can run Novor independently of TPP and later import the results via conversion to the pepXML format (see below).

Novor can only read mgf files; please convert your mzML files by using the Convert mz[X]ML Files utility before starting the search.

In order for Petunia (the TPP interface) to be able to launch Novor searches, please follow the following steps:

• After downloading Novor, place the novor/ folder alongside the other TPP binaries -- typically under C:\TPP\bin\
  • Novor can also be installed in a different location, but this requires extra configuration steps to work in TPP. Contact the mailing list if you need assistance.
• If you get a Java language error, you may need to edit the Apache configuration file shipped with TPP (typically C:\TPP\conf\httpd-tpp.conf), and add the path to your local Java installation under the <Directory "C:\TPP"> section:

 SetEnv JAVA_HOME C:\PATH\TO\JAVA\INSTALLATION

Editing parameters

You can edit Novor parameters files using a text editor or in Petunia -- just make sure that the first comment line in the file contains the words Novor and parameters.

Conversion to pepXML

There is an option to automatically convert Novor output to pepXML in the Novor search page. There is also a stand-alone page that enables the conversion of any Novor search results file to pepXML. Make sure that the path to the mzML raw data is correct, otherwise links to view spectra will be broken.