Peptide counts for multiple label-free sample comparisons

[potockym]

Hello, I want to use DEqMS to analyze my LFQ dataset, which consists of five samples (each in triplicate) and analyze the DEPS among all ten possible comparison pairs. Should I use the values from the total dataset for the peptide min count, or should I always use minimum peptide counts relevant only for the compared sample pairs?
Thanks
Martin Potocky

[yafeng]

@potockym Hi, I recommend to use minimum peptide counts relevant only for the compared sample pairs.

Yafeng