I have a control and test with two biological replicates for each. After running the samples in mass spec with three technical replicates or three injection for each sample I have 6 raw file for control and 6 for test. During the proteome search how the search should be performed. Should all the files be searched together? or control and test should be searched differently? What is the actual way of analysis. Someone please help me out in this. I have done label free quantitative proteomics.