Question regarding the generation of mutated peptide sequence

[ec-ho-ra-mos]

Hello Professor Vadim!

I have two questions regarding this statement from the DIA-NN paper: "For each target precursor in the spectral library, a decoy precursor is generated, if not provided in the library. By default, this is done by replacing the fragment ion m/z values of the target precursor assuming the amino acids adjacent to the peptide termini were mutated (GAVLIFMPWSCTYHKRQEND to LLLVVLLLLTSSSSLLNDQE mutation pattern is used)".

1. How exactly does the GAVLIFMPWSCTYHKRQEND to LLLVVLLLLTSSSSLLNDQE mutation pattern work? Can I ask for a detailed explanation/guide on how this mutation pattern works? For example, I have 3 peptides "PEPTIDEEE", "SCTYNQQQ", and "AAAAAAAEEEEEELLLL", how will these peptides be mutated according to this pattern?
2. By this statement, specifically the part about the fragment ion m/z, does this means that the fragment ion m/z from the mutated peptides are used instead of the supposed correct fragment ions for the target, is my understanding correct?

My rationale for this question is I want to generate decoys using the same pattern as the one from DIA-NN.

A similar discussion regarding this question was raised in December 2021. But I don't think OP's question, nor mine, was answered sufficiently.

Thank you very much for your attention,
Echo

[vdemichev]

Hi Echo,

1. Each amino acid adjacent to the termini is replaced by the respective replacement aa (e.g. G replaced with L and L replaced with V) using the pattern.
2. Yes.

Best,
Vadim

[ec-ho-ra-mos]

Hello Professor Vadim,

Thank you very much for your reply!
Echo