Adding Custom Modifications

User created modifications can be added to Metamorpheus. New modifications can be selected in Metamorpheus as variable, fixed or for use in G-PTM-D. The existing modifications are organized in text files in the "Mods" folder of MetaMorpheus. This is best accessed directly through the MetaMorpheus GUI application by selecting from the drop-down menu tab 'Data' found at the top of the form. You can access it directly in Windows using the File Explorer in the \User***\AppData\Local\MetaMorpheus\Mods folder. Command-line users will find a mods folder in the MetaMorpheus root directory. The user is free to add modifications by either editing those files or by creating a new text file (preferably using Notepad++, which helps one get the syntax correct). User added custom mods WILL BE OVERWRITTEN during software updates unless the modifications are added to a new text file (e.g. user_custom_mods.txt).

Each modification contains a number of fields designated by a two letter code (see list below). Information for these fields follows the letter code separated by three space characters. EACH FIELD VALUE PAIR MUST BE ON A SEPARATE LINE

* AC Accession

An accession number of frequently supplied by the primary databases (e.g. UniProt and Unimod).

* CF Chemical formula (required if no MM is supplied/defined)

This is the chemical formula of the added or removed atoms. This is required but the mass shift used is specified by MM. The particular isotope of the element can be specified in curly braces following the element name. For example, carbon-13 is written as C{13} in the chemical formula. The number of atoms is specified after the closing brace. Five carbon-13 atoms is written as C{13}5.

* DI Diagnostic Ions

Certain PTMs (e.g. acetylation or glycosylation) produce small diagnostic fragment ions that can be detected in MS/MS spectra. These ions can serve as useful indicators of the presence of the corresponding PTM. This feature is currently disabled.

* DR External database links

* FT Feature key

Used in the UniProt ptmlist but not needed for custom mods in MetaMorpheus

* ID Identifier (Required)

This is the text used to describe the modification in the output.

* MM Monoisotopic mass (Required if CF is not supplied/defined)

The exact atomic mass shift produced by the modification. Please use at least 5 decimal places of accuracy. This will override the monoisotopic mass described in the chemical formula because there are cases where the mass of the mod and the mass shift from the mod are different (e.g. trimethylation has mass of 43 but mass shift from trimethylation is 42).

* MT Modification type (Required)

This specifies which modification group the modification should be included with. Existing modification types are described here. The user is free to designate their own type, which creates a separate list.

* NL Neutral loss (if any)

Certain PTMs (e.g. phosphorylation) have labile modifications that can be lost during ionization. The peptide parent mass in MS1 may be seen with or with out the modification. Specifying neutral loss tells MetaMorpheus to take this phenomenon into account.

* OM Masses seen in the histogram

* PP Position of the modification in the polypeptide (Required)

Choose from the following options: Anywhere.; Peptide N-terminal.; N-terminal.; Peptide C-terminal. DON'T FORGET THE '.'

* TG Target (Required)

Amino acid letter code capitalized or written out. Muliple targets separated by " or ". The capital letter 'X' may be used to mean any amino acid.

* // Break between modifications