Determining Species-specific Peptides in DiaNN

[sgarcia2099]

Hello, We are attempting to assign peptides to either the mouse or human proteome. To do this, we were using the human, mouse, or both designation in the proteins.name column of the DIA-NN report.tsv file. However, when we search for peptides that should be shared between mouse and human species they are coming up as only human. Does DIA-NN have the ability to evaluate individual peptides for species specificity? In general, how does DIA-NN assign species to each peptide when multiple proteomes are searched simultaneously (i.e. human and mouse)? Thank you!

[vdemichev]

The Protein.Names column in the output report is based on inferred proteins (with protein inference following the maximum parsimony principle). So either

• turn off protein inference
• or, if you need protein inference but just want to filter out anything matched to both human and mouse proteomes, can match all entries in the Protein.Ids column to either FASTA using some R package or

Best, Vadim