ZNova Mass Configuration File

ProMass uses a text configuration file to store the masses of the amino acid, nucleotide, termini, impurities, and modified residues. The text file is called znova_masses.ini and it can be found in your ZNova install directory (e.g., C:\Program Files\ProMassXcali\ZNova\znova_masses.ini). All of the standard amino acid and nucleotide groups are provided, but you can also create your own amino acid or nucleotide groups by editing the znova_masses.ini file. Notepad can be used to edit znova_masses.ini. The main purpose of znova_masses.ini is to provide a means for ProMass to calculate the masses of sequences that you enter into the BioSequence field of the Xcalibur sample list. When you enter a biomolecule sequence in the BioSequence field of the sample list and define the sequence type, ProMass will look up the mass of each residue in your sequence in the znova_masses.ini file and calculate the mass of the sequence and treat it as a target mass. Because there are many types of sequences that you can define, the configuration file has a series of sections defining the masses for the various residues of each type. Each section heading is denoted by a text string in brackets e.g., [oligoAvgMass]. The type of sequence for each BioSequence string in the Xcalibur sample list is specfied in the Target Info field of the sample list, as described in a previous help topic. A summary of all section headings for each type of sequence is shown below:

These sections are used when sequence = peptide, protein, or amino acid
[aaIsoMass]: monoisotopic masses of amino acid residues
[aaAvgMass]: average masses of amino acid residues
[aaImpurities]: masses of known impurities for amino acid sequence types

These sections define the masses of terminal groups and other related species. Terminal groups are only used with amino acid sequences.
[isoMass]: monoisotopic masses masses of terminal groups
[avgMass]: average masses of terminal groups

These sections are used when sequence = oligo
[oligoIsoMass]: monoisotopic masses of nucleotide residues using IDT base notation
[oligoAvgMass]: average masses of nucleotide residues using IDT base notation
[oligoImpurities]: masses of known impurities for oligo sequence types

These sections are used when sequence = formula or molecule
[chemIsoMass]: monoisotopic masses of chemical elements
[chemAvgMass]: average masses of chemical elements
[chemImpurities]: masses of known impurities for chemical formulas

This section is used when no sequence type has been defined
[Impurities]: masses of known impurities used when no sequence type is specified

The PTMs section defines the masses of common post-translational modifications

Here are some additional guidelines for editing the znova_mases.ini file, should you need to:

The # character represents a comment. Put # at the beginning of a line to create a comment line.

DO NOT modify the section heading names [the ones within brackets].

Comments and species definitions should be on separate lines.

Definitions are case insensitive, therefore 'A' is the same thing as 'a'.

You use single alphanumeric characters (0-9, or A-Z) to define amino acid residues.

For amino acids and oliognucleotides, modified residues can be defined using the format: /mod/ = mass using alphanumeric characters between the slash characters, e.g., /DMT/ = 303.2

Definitions of terminal groups and impurities can contain multiple alphanumeric characters, e.g., H2O = 18.0152

If you enter a new definition be sure to enter masses in the corresponding sections for both monoisotopic and average masses.

Impurities can be defined for each type of residue. Impurity masses are entered as delta masses from expected target masses. If no sequence type or BioSequence is known, the impurities under the heading [Impurities] are used.

Oligonucleotides are defined with IDT's base notation use the format: A, A*, mA, mA*, rA, rA*, or +A, depending on the type of nucleotide. See http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/ for more info about IDT's base notation format. Internal modifications and termini are specified using the /mod/ = mass format.

If a known impurity definitition is preceded by a ' * ', the abundance of that particular species will be ignored in any purity estimate calculations.

Post-translational modifications are defined in the [PTMs] section. Comment out all PTM definitions to disable PTM searching. New PTM definitions may also be added.