ISA-guided domain specific workflows. A possible workflow for an ISA-Tab augmented experiment design and execution. ① The experiment is designed with e.g. the ISAcreator to define the samples. ② The experiment is performed and samples are collected. ③ The sample names are transferred to the machine, e.g. a mass spectrometer (MS), to run the assays. ④ Assays are performed. In the MS example, it often occurs that the MS instrument software allows to copy & paste into its sample table, and creates a report (including MS filenames) that can go into the ISA-Tab assay information. ⑤ Domain specific R packages, such as xcms for MS, process the raw data. ⑥ The Risa objects are augmented with the results of the assay and the completed ISA-Tab dataset can be written back to disk.