Upon execution of the *.jar or *.bat file, the program is started by opening a dialogue window to select the data for processing. First, a database has to be selected. This is the database/FASTA file that was used for search of the LC-MS/MS data.
Next, search results are loaded. DigDig was primarily based for *.csv based results from MASCOT but we tried our best to make it compatible with other search engines - PEAKS, FragPipe, Byonic, SpectroMine and Waters PLGS search results. If you wish to use the DigDig for another types of search results, or encounter problem with reading of your search results, please contact the authors. We will be happy to adopt the program to your specific files.
The naming conventions defined under 2. Input data ensure the replicates and experimental conditions are automatically recognized. There is now no other way how to sort and organize the replicates and conditions in the program, so please keep this in mind when collecting or renaming the data.
If there is no mismatch between the entries in the search results and the database, the program window appears.
If the database was modified and some entries were changed or deleted, the program starts a window to either skip a particular entry or localize it within the list of database entries. Skipping some entry is linked to a command window message “Accession XXX_XXXX not assigned to any protein, just skipped.”
Alternatively, select “Cancel” and skip all mismatches. These are then written in the command window (if you run the program via the batch file with the command window open) - “Ignoring unknown accession when reading digest result: XXX_XXXX”
Currently, the program menu has only the File section, containing several additional actions. To start a new session, where new database and analyses are selected. To load new database (FASTA file) or to load another analyses for the current database in use. The pre-uploaded database remains active but another search result files can be uploaded. The last two options are related to repetitive sequences found in analyses and offers look into these repetitions in separate window, providing information about protein accession, amino acid sequence, and its start and end position. This list can be exported as a separate, structured and tab-delimited file.
We do not provide search result files from engines other than MASCOT. However, the formats mentioned above were tested - see brief description HERE.
This was made possible thanks to the generous support of Franta Filandr (IOCB, Prague), Oskar Knittelfelder (Bruker Daltonics), and Stella Ritorto (ProFound Therapeutics). Once again, many thanks!
We also thank Valča for her creative help with designing the logo.