CycloBranch
Modifications Editor

Modifications Editor

The editor is opened using the command "Tools -> Modifications Editor" from the Main Window. Use F1 to open this help.

Changes in the editor do not impact the settings of the engine until they are saved !

modificationseditor.png
Modifications Editor

Toolbar

New Database (CTRL + N)

Create a new database of modifications.

Open Database (CTRL + O)

Open a database of modifications.

Save Database (CTRL + S)

Save the database of modifications.

Save Database As... (CTRL + D)

Save the database of modifications with another file name.

Import Database (CTRL + I)

Import a database of modifications.

Close (Esc)

Close window.

Insert Row (Insert)

Insert a new row at the bottom of the table.

Remove Selected Rows (Delete)

Remove checked rows.

Select All (CTRL + A)

Select all rows.

Unselect Rows (CTRL + U)

Unselect all rows.

HTML Documentation (F1)

Show HTML documentation.

Text Filter

See details here.

Columns

  • Name - Name of an N-terminal or a C-terminal modification.
  • Summary Formula - Summary formula of a modification (e.g., H2C2O for acetylation or HNO-1 for amidation). Negative numbers of atoms are supported (e.g., H-2O3N-5 means remove two hydrogens, add three oxygens and remove five nitrogens).
  • Monoisotopic Mass - Monoisotopic mass corresponding to a modification. The value is recalculated when the summary formula is changed.
  • N-terminal - When checked, the modification is considered to be N-terminal.
  • C-terminal - When checked, the modification is considered to be C-terminal.

Format of Modification Databases

The list of modifications is a text file (*.txt) containing one modification per line. Each line contains the following items separated by tabulars:

  • name of a modification
  • summary formula of a modification (important: an exact mass of the block is calculated from this value)
  • monoisotopic mass (the value is ignored; the mass is automatically calculated from the summary formula)
  • the value "1", when the modification is N-terminal; "0" otherwise
  • the value "1", when the modification is C-terminal; "0" otherwise

A line starting with the hash '#' is a comment which is not processed.


List of Available Modification Databases

The following pre-defined databases of terminal modifications are available in "Modifications" folder:

LocationContent
acetyl.txtacetylation
acetyl_amidated.txtacetylation and amidation
amidated.txtamidation
default_inhouse.txt4 modifications (compiled in-house)
ethanolamine.txtethanolamine
ethanolamine_formyl.txtethanolamine and formyl
norine-terminal-blocks.txt7 terminal blocks/modifications compiled from Norine (version July, 2013)
putrescine.txtputrescine
tutorial5.txt4 modifications used in Tutorial 5
customDownload Template for Excel