# Search parameters.

# Enzyme
## Only 'Trypsin' is supported currently.

enzyme = Trypsin

# MS2 Spectrometer
## fragmentation can be CID or HCD
## massAnalyzer can be Trap, TOF, or FT
## Orbitrap instrument corresponds to CID-Trap, CID-FT, or HCD-FT
## QTof instrument corresponds to CID-TOF.

fragmentation = CID
massAnalyzer = Trap

# Mass error tolerance
## precursorErrorTol can use both the formats of 0.1Da and 15ppm
## fragmentIonErrorTol only supports the format 0.1Da in current version

fragmentIonErrorTol = 0.5Da
precursorErrorTol = 15ppm

# PTM
## Variable modifications will make algorithm consider both modified and the original residue
## Fixed modifications will turn off the unmodified residue from consideration
## A comma-delimited list of IDs can be used here.
## See http://rapidnovor.com/wiki/Built-in_PTMs for a list of built-in PTMs and their IDs

variableModifications = Oxidation (M)
fixedModifications = Carbamidomethyl (C)

# Forbidden residues
## It is suggested to disable residue I because it is the same as L
## The 21st amino acid U should be disabled too because it is so rare that adding
## it to de novo sequencing will cause many more false positives than true positives.

forbiddenResidues = I,U

# Customized algorithm parameters
## The novorFile parameter is for the most advanced users only.
## Novor uses advanced machine learning algorithms to learn patterns from existing data,
## and utilizes those patterns in its de novo sequencing. These patterns are described by
## thousands of parameters and stored in a .novor file.
## By default, one of the built-in .novor files will be chosen by the algorithm
## according to fragmentation and massAnalyzer. This should be sufficient for most users.
## However, because of the inevitable deviation in the data caused by the instruments and
## labs procedures, more advanced users may want to contact rapidnovor.com to train a
## customized .novor file for their specific instrument and lab procedure. This usually will
## further improve Novor's accuracy on data produced specifically in their labs.

# novorFile = external.novor