Search specific peptides in proteomes

[LKittinun]

Dear Vadim,

I am conducting an experiment in which the cells were engineered with specific peptides, and I monitor changes in the proteomes. On top of that, I want to confirm whether particular peptides used to engineer are present in the cells. I did a standard tryptic digest experiment in a wet lab part. I would like to know if:

• It is feasible to search for targeted peptides in this setting.
• If so, can I just concatenate the target peptides to the standard Uniprot FASTA and predict the library. Or is there any specific workflow I must consider?
• How should I control the FDR in this setting.

Regards,
Pete

[vdemichev]

Hi Pete,

DIA-NN will search any FASTAs you supply to it, i.e. just need to provide a separate FASTA with peptides of interest. FDR will be controlled just fine automatically, except you may want to filter by PEP instead of Q.Value.

Best,
Vadim