vdemichev
commented
2 months ago Yes, it's more stringent, at both precursor & protein level, as well as the pg_matrix is in addition filtered at 5% run-specific protein group q-value.
Open Raghothama1 opened 2 months ago
vdemichev
commented
2 months ago Yes, it's more stringent, at both precursor & protein level, as well as the pg_matrix is in addition filtered at 5% run-specific protein group q-value.
I searched DIA-NN versions 1.8.1 and 1.9 containing two replicates of DIA-MS data for the K562 digest. The Venn diagram shows more peptides found in the report.tsv file from version 1.9, but the number of protein groups in the report.pg_matrix is lower from version 1.9. Is version 1.9 more stringent?