There are two types of modifications, fixed and variable. Fixed modifications will
be added to every residue that can be modified by the given modification, while the variable modifications
are sometimes added and sometimes not. Which type to choose depends on your experimental setup.
You can add multiple modifications of each type, but remember that the more variable modifications you
add the more complex the search becomes which increases the risk of false positives.
Initially only the most used modifications are shown. To show all modifications simply select 'All
Modifications' in the drop down menu above the list of modifications. Here you can also see more
details about each modification.