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Table 1 The command line options of mres2x. Parameters for setting the Mascot™'s username, changing line break characters as well as debugging mode exist, too. The usage of mres2x is: mres2x -d destination -o type [-rvfpSuU] filemask_of_input_files, where the last parameter defines the input file(s) including the path and can even be a single file. The input must be in original Mascot™ format, not HTML. The files from the file mask must be in the same directory if the output format is not tab. In case of tab format output, the destination must be a single file, otherwise a folder. mrex2x explicitly expands input file masks. A description of the parameters also can be found in the file Overview.html (see additional file 1) included in the source code package.

From: Efficient analysis and extraction of MS/MS result data from Mascot™ result files

Option Parameters Explanation
type s_dta
m_dat Tab
Describes the output format. Supported types are:
s_dta Sequest™'s dta format. Only spectra data will be exported.
m_dat split the input into several output files in Mascot™'s output format, one for each query.
Tab write out a tabbed format for direct database upload.
-r   Use CR LF instead of LF as linefeed in data blocks. Some OS need special line feed characters in text files.
-v   Increase verbosity mode by one per occurrence of -v. A maximum of two -v is allowed.
-f   Overwrite files/allow usage of non-empty directories. Usually, the destination directory must be empty.
-p   Preserves files on unsuccessful program termination. Useful for debugging purposes.
-S   Show message indicator even if stderr is a terminal.
-u name Set the username to name, if no entry is present and if the tab output format is selected.
-U name Set the username to name in all cases if the tab output format is selected. This allows changing the username in the result files of Mascot™.