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Add docs for isobaric formula modifications #159

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Add docs for isobaric formula modifications #159

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15 changes: 14 additions & 1 deletion docs/source/userguide/configuration.rst
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Expand Up @@ -81,7 +81,20 @@ preferably provide the formula instead of a mass shift, as the mass shift can al
be calculated from the formula, but not vice-versa, and some feature generators (such as DeepLC)
require the modification formula.

And example of the :py:obj:`modification_mapping` could be:
.. role:: raw-html(raw)
:format: html

Formula modification labels can be defined with the ``Formula:`` prefix, followed by each atom
symbol and its count, denoting which atoms are added or removed by the modification. If no count is
provided, it is assumed to be 1. For example, ``Formula:HO3P`` is equivalent to ``Formula:H1O3P1``.
For isotopes, prefix the atom symbol with the isotope number and place the entire block (isotope
number, atom symbol, and number of atoms) in square brackets. For example, the SILAC 13C(2) 15N(1)
label (`UNIMOD:2088 <https://unimod.org/modifications_view.php?editid1=2088>`_)
would be notated as ``Formula:C-2[13C2]N-1[15N]``, meaning that two C atoms are removed, two
:raw-html:`<sup>13</sup>C` atoms are added, one N atom is removed and one
:raw-html:`<sup>15</sup>N` atom is added.

An example of the :py:obj:`modification_mapping` could be:

.. tab:: JSON

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