Two procedure files were created to automate the processing of mass spectral (MS) data files. The procedure file, RJR, was used to set up the sequence of mass spectral data files to be processed, to input the parameters for printout format, and to automatically execute the processing of the mass spectral data files. The other procedure file, RJRAQ, was used to execute the processing of mass spectral data. RJRAQ produced header information of the mass spectral data files and the integration information, generated graphic displays of the total ion chromatogram (TIC), mass spectra, and library search results, and provided hard copies of all textual reports and graphic outputs.