Hello,

I would highly appreciate if you could guide me about my following questions about using the CRAPome database (https://reprint-apms.org/?q=chooseworkflow) for filtering proteomics datasets:

1) What is the logical score that I can use as the CRAPome cut-off score (filtering threshold) for the filtering of the proteomics dataset? I am confused about it as different papers used different scores.

2) Also, regarding the CRAPome cut-off score, the score of which of the "Num of Expt. (found/total)", "Ave SC" , and "Max Sc" should I use for the filtering non-specific proteins?

3) From the updated version of CRAPome database (V2.0), some of important proteins have Num of Expt. (found/total) of around 400-450 (out of 716). But, I do not want to remove them as contaminant. They should be remained in the dataset as they have important roles in my protein interaction network. Any suggestions/solutions that how I can scientifically keep these important proteins while having high Num of Experiment (found/total) in the CRAPome database are much appreciated.

Many thanks for your valuable help.

Best wishes, Farah