In order to adapt the process to the search it is necessary to provide some information about it to PeptideShaker.
Some parameters are set by default, while some have to be set manually.
If the identification files were generated using
SearchGUI, settings will be loaded automatically!
The search parameters are mandatory for the import of identifications as well as for their processing and display. Set here the enzyme used, the number of allowed missed cleavages and the fragment ion mass tolerance.
The modification profile is a project-dependent set of expected modifications. PeptideShaker will check this
list when a PTM is found in the identification results. Modifications can be grouped into families and will then be
processed together.
It is possible to change the family and short names used for a given modification. Simply click the cell you
want to edit. In the same way, the color used for a given modification can be changed by clicking on the current
color. The names and colors set here will be used throughout the tool.
It is vital that two different families do not contain PTMs of the same mass!
The modification profile can be saved and opened from here as well.
Modification profile details can be changed later from the Edit menu.
When exporting data to PRIDE each PTM has to be mapped to a given PSI-MOD CV term. The default PTMs are already
mapped but user defined PTMs have to be mapped by the user. If this is not already done in SearchGUI,
the mapping can be added here by right clicking the given row and selecting Edit.
Click the PSI-MOD link to get further details about PTM.
For simplicity, it is also possible to load the standard settings from a SearchGUI file.