Are any recommended tools to deal with many missing values in the phospho proteomics data matrix

Question

[alwayshope]

Dear guys,

Are any recommended tools to deal with many missing values in the phosphor proteomics data matrix?

When searching the net, most direct to the imputation (median, k-nearest neighbor, etc. ), while if the samples 3 replicates for treat1 all missing (treat2/3/4/5/6 partial missing), it seems not possible to impute the values for the treat1 accurately...

It's a bit surprising when looking at the Excel file of the phosphoproteomics abundance matrix, missing values are now and there...

Thank you very much for your guidance!