Input files for DigDig are the database that was used for search of the LC-MS/MS data and the result files. Currently, it was built for MASCOT search results, which are exported in the *.csv format.
The filename of the search result is very important as it is used for automatic recognition of the experimental conditions and replicates. Anything up to the last “underscore” ( _ ) in the file name is considered as description of experimental conditions. Hence if you keep exactly the same string before the underscore, these files will be considered as replicates. Anything after the last underscore is not considered here, but the full name of the file will be displayed in the program so you can easily differentiate the individual replicates.
Example: file name MY_EXPERIMENTAL_CONDITIONS_2024-01-02-rep01 will result in conditions named MY_EXPERIMENTAL_CONDITIONS
There is currently no other option to group the analyses and recognize replicates or experimental conditions.
For applications like HDX-MS where one or few proteins are studied we strongly recommend making larger, not just single/few protein database, by adding at least the cRAP sequences - https://www.thegpm.org/crap/. This allows you to run decoy search and filter the data according to their statistical significance. For the export, we then recommend exporting the data with FDR better (lower) than 1% and MASCOT score reaching at least 20-25.
Then the options “Start”-“End” delimiting the peptide limits must be selected.
