Novor Command Line

Novor supports all major operating system, Windows, Linux and Mac OSX. To make the command line execution easier, we provided the shell scripts (novor.bat for Windows and for Linux and Mac OSX) in the Novor package in the corresponding OS directories. The examples in this article describes the Novor command line on Windows. Running Novor on Linux and Mac OSX should be very similar.

Command line options

The simplest command to run Novor is as follow:

novor.bat -p params.txt YOUR_MGF.mgf

The above command line will use search parameters specified in params.txt, perform de novo sequencing on YOUR_MGF.mgf file and generate result in the same directory of the MGF file with name YOUR_MGF.mgf.csv.

You can specify Novor options in any order.

Novor supports the following options


The search parameter file. A sample parameter file can be found under the software package.


The name and path of the output result file. If omitted, a csv file with the same name as the input spectrum file will be generated under the input file directory. If the file already exists, user can choose to overwrite the file or exit Novor during the process.


Force overwrite without prompting for confirmation when output file exists.


Specify the file containing a list of custom modifications. The file is in CSV format. The explanation of the columns can be found here.

Below is an example, my-mods.txt:

mymod1, mymod_short, mymod_long, -r-, *, -HN+O, 0.98

mymod1 is the “ID” of the modification. It has to be unique. It will be used in the search parameter file later on.

mymod_short and mymod_long are descriptive names. mymod_short will be used in the result file indicating such a modification happened.

-r- indicates that the modification will happened at the residue’s side chain and * means the modification can happen on any residues.

-HN+O is the molecular difference defined as the change of atoms. If this is defined, the mass difference of the modification will be ignored.

0.98 is the mass difference the modification caused. Either the molecular or the mass difference must be defined for the modification. In the situation that one of them is omitted, it is important to keep the comma (,) in place to form the correct format. Below is the same modification definition with the molecular difference omitted, noticing the two adjacent comma.

mymod1, mymod_short, mymod_long, -r-, *, , 0.98

Here is a longer command with all command line options in use:

novor.bat -p params.txt -o resultsmyresult.csv -f -m my-mods.txt MY_MGF.mgf

Search parameter file

The search parameter file used in Novor is in Java properties file format. In essence, it defines a name-value pair on each line as name =  value. Any  empty lines or lines starting with hash sign (#) will be ignored. We strongly recommend to retain a copy of the params.txt file included in Novor package and use it as a starting point for your customized search parameter file.

Most part of the file are self explanatory. For example, the following lines define the enzyme, mass analyzer, precursor and fragment ion tolerance:

enzyme = Trypsin
fragmentation = CID
massAnalyzer = Trap
fragmentIonErrorTol = 0.5Da
precursorErrorTol = 15ppm

Below is an example on how to specify modifications. Use comma (,) as the delimiter to separate multiple modifications. The modifications used here can either be built-in modifications or the custom modifications introduced by the -m command line option.

fixedModifications = Carbamidomethyl (C)

variableModifications = Oxidation (M), Deamidated (NQ), mymod1