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PTMs

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touzet edited this page Jan 9, 2025 · 4 revisions

Peptide tables include a field labeled PTM, which is utilized to describe the post-translational modifications (PTMs) applied to the corresponding peptide. PAMPA recognizes three types of PTMs:

  • hydroxylation of prolines, indicated by the single-letter code 'H',
  • deamidation of asparagine and glutamine, indicated by the single-letter code 'D',
  • phosphorylation of serine, threonine, and tyrosine, indicated by the single-letter code 'P'.

The PTM description is a concise representation of the number of each of these modifications. For instance, '2H1D' signifies two hydroxyprolines and one deamidation, '1P4H' represents one phosphorylation and four hydroxyprolines, '2H' corresponds to two hydroxyprolines without any deamidation and phosphorylation. When no PTM applies, the description should be '0H'.

In general, PAMPA will automatically compute the theoretical mass of a peptide sequence given that the PTM description is given. The mass modification is as follows:

  • H : 15.994915 Da
  • D : 0.984016 Da
  • P : 79.9663 Da

When the PTM description field is left empty in the peptide table, it signifies that PTMs are not specified. In such cases, PAMPA attempts to infer PTMs based on the following rules:

Hydroxyprolines: The number of is determined empirically from the total number of prolines in the peptide. We use the following formula: Let 'p' represent the number of prolines in the peptide, and 'pp' represent the number of prolines involved in the pattern 'GxP'. If the difference 'p-pp' is less than 3, then 'pp' hydroxyprolines are applied. If 'p-pp' is 3 or greater, 'pp' hydroxyprolines and 'pp+1' hydroxyprolines are applied.

Deamidation: For each peptide marker, it is possible to apply one deamidation in a systematic way with the --deamidation option (available in both PAMPA CLASSIFY and PAMPA CRAFT). This modification will apply only on peptides whose sequence contains at least an asparagine or a glutamine. It is possible to specify the set of markers impacted by the modification using a limit file (see Limiting searches).

Phosphorylation: When needed, phosphorylation should be added manually in the peptide table, by editing the PTM description.

In all cases, it is possible to edit the PTM field manually in the peptide table.

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