What is the reason for the requirement of at least 2 experiments for LFQ in MaxQuant?
I am analyzing plasma proteomics using Mass spectrometry. My cohort contains plasma samples from family members with the disease and remaining members without the disease. When I am trying to quantify my data using Label Free Quantification (LFQ) available on MaxQuant, I get an error (screenshot attached).
I want to know the reason for requiring at least two experiments for LFQ? What type of two samples are required? Can I use diseased and healthy individual samples? Does it matter which sample I am using as control (I have multiple healthy samples from a family)?
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