Systems biology requires comprehensive data at all molecular levels. Until recently the determination of cellular protein levels was lagging behind the corresponding mRNA measurements. Now it is becoming feasible to extract system-wide quantitative data for nearly the complete proteome and for ten-thousands of posttranslational modifications. Underlying the recent success of the field are developments in computational proteomics, which now allow highly sophisticated and completely automatic analysis of raw MS data and streamlined bioinformatic and systems-level interpretation of the results. MaxQuant is an all-encompassing end-to-end computational workflow solution for quantitative proteomics. In this presentation the structure of MaxQuant and its crucial algorithmic parts are described as well as a perspective for future developments will be given and challenges will be discussed.