Figure 5. Flexible workflows through support of standard proteomic data exchange formats. In the figure, mzML, mzXML and mzData are standard XML formats for MS/MS data. DTA is the generic format for SEQUEST input. MGF is the Mascot Generic Format. pepXML is the standard XML format for database search output. OUT is the generic format of SEQUEST search output. Conversions indicated with solid arrows are accomplished autonomously within HTAPP while the dashed lines indicate the tasks that require user intervention. Post-processing of additional mass spectrometer specific raw data formats is provided through support of mzML, mzXML and mzData formats. Database search engines beyond SEQUEST and Mascot can be implemented by converting DTA to a particular format for that search engine and exporting search output in pepXML format, as is illustrated for Mascot here.