PTM Site Inference

Introduction

This dialog displays the quality of the PTM localization onto the peptide sequence. It is possible to change the PTM site and the assignment confidence.

Note that PTM specific study with PeptideShaker is at its genesis. Feel free to contact the developers if you have special needs.


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Peptide Level Inference

The quality of the PTM localization on the sequence can be 'Not Found', 'Random', 'Doubtfull', 'Confident' or 'Very Confident'. For every peptide, PeptideShaker gives a confidence level which can be manually changed by the user in this dialog. Note that only validated hits will be taken into account, non validated hits will be marked as 'Not Found'.

Every PTM is mapped onto the peptide sequence and subsequently protein sequence based on the user defined color coding. Note that confident and very confident modifications will be displayed with a color background whereas secondary modification sites will be displayed with a white background.


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PSM Level Inference

The peptide level modification sites are deduced from the various PSM rattached to this peptide. These are displayed in the Potential modification sites table.

Every column of this table represent an amino acid of the peptide sequence. The first line allows you to manually select the primary (confident) modification sites while the second is used for secondary modification sites.

The confidence in a modification site assignment is computed using PSM level scores. The combination of these scores, color coded in the table where every line represents a PSM, is used to deduce the potential modification sites. The peptide level scores subsequently calculated can be inspected in the modifications tab.


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