identification of peptides from a peptide library

[marthanik]

Hello,

we have generated an HLA-peptides library using PeptDeep-HLA for the prediction of peptides and alphapeptdeep for library generation and conversion to .tsv for compatibility with DIANN. Then we tried to use it with some already acquired sample spectra to test for peptide identification. Despite the fact that the test.log file mentions identified IDs at the 1% FDR for both tested sample spectra after the second pass, eventually the pr_matrix.tsv is empty. Any idea why this might be happening? Are there any additional options that we need to consider during running DIANN?

Thanks!

Martha

test.log mod.txt

[vdemichev]

Hi Martha,

pr_matrix is filtered also at global protein q-value, which probably is not calculated correctly due to lack of protein annotation. The solution is simple: please just use the main report.

Best, Vadim