Input files for DigDig are:
- database that was used for search of the LC-MS/MS data
- search results (e.g. *.csv results from MASCOT server)
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.
Example datasets are available here.
If you are interested in the *.mgf files or raw data, please contact the authors
For applications like HDX-MS where one or a few proteins are studied, we strongly recommend making a larger, not just single/few protein database, by adding at least the cRAP sequences - https://www.thegpm.org/crap/. This allows you to run a decoy search and filter the data based on statistical significance.
Exporting data from MASCOT
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.
PEAKS results
DigDig can read and load search results from the db.protein-peptides.csv file.
FragPipe results
DigDig can read and load search results from the peptide.tsv and/or psm.tsv files.
Byonic results
DigDig can read and load search results from the output.spectra.txt file and from Spectra sheet in *.xslx output file saved in *.csv format.
SpectroMine results
DigDig can read and load search results from the *.tsv / *.csv report file.
Waters PLGS results
Search results from Waters PLGS exported into a *.csv file are compatible with DigDig.
Agilent Spectrum Mill results
Search results from Spectrum Mill exported into a *.ssv file ( peptideExport.CS.1.ssv or PSMexport.1.ssv ) are compatible with DigDig.