The procedure for Spo11 data is based on the peptide intensities reported in the evidence file provided by MaxQuant: 1) peptide intensities are normalized using the variance stabilization transformation (bioconductor package vsn) 2) Doing Top3, I chose not to impute any further the missing peptide intensities 3) Taking the protein groups identified by MaxQuant and reported in the proteinGroup file, the protein intensities are calculated as the mean of the three most intense peptide of the leading razor protein. 4) If no protein is found in a sample, the reported intensity is zero 5) Differential analysis using the empirical Bayes statistics from the bioconductor limma packed is performed with the false discovery rate set at 0.01. Most proteins showing significant difference are only in SPO11. MaxQuant proteinGroups and evidence file are joined as sheets in the Mass Spec Spo11_raw.xlsx. The first sheet, "Differential Analysis", marks the proteins significantly different in SPO versus CTR (first column), under the test condition described above. The next 6 columns are the Top3 intensities in each sample. You may also want to ignore proteins with Q>0 (column BL in the file).