I have more than 250 GB of mass spectrometry data [SYNAPT G2-Si Mass Spectrometry (from Waters)] from investigating bacterial whole proteome in a label-free quantification experiment, conducted at 5 time points: 0 minutes, 15 minutes, 30 minutes, 45 minutes, 60 minutes. I did 5 replicates of control (untreated samples: 0 minutes) and 5 replicates treated same other times points (15,30,45,60 minutes). I need to conduct differential analysis at each time point versus the control and obtain statistical significant proteins that are increased or decreased.
Any suggestions for tools/softwares that can get the job done accurately and fast (preferably for free) ? Can you integrate data to KEGG software as well ?