Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Home Page:https://msfragger.nesvilab.org

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output_report_topN adjusted when data_type = 0

asalt opened this issue · comments

commented

Hello. I am running a search with data_type = 0 (I did not set this variable, set by default). I notice this message with regard to output:

data_type = 0 and output_report_topN > 1. Change output_report_topN to 1.

Is this intended behavior? The changelog says this adjustment is performed for DIA, but does this also apply to DDA (data_type 0) ?

Yes, this is an intended behavior in 3.4. We will stop changing it to 1 in the future release.

Best,

Fengchao