Multidimensional separation experiments investigate complex proteomes by applying multidimensional chromatography to the samples before acquisition in the mass spectrometer. Typically, this process results in several dozen or even a few hundred fractions that are separately analyzed by LC/MS, resulting in one raw data file per sample fraction. Analyzing gel slices or performing in-depth follow-up acquisitions also results in multiple fractions. Because all these fractions belong to the same sample, the Proteome Discoverer application can process all raw data files from these fractions as one contiguous input file and generate a single result file. For detailed information about processing multidimensional separation experiment samples, see Add fractions.