hbarsnes
commented
6 months ago Have you had a look at the PeptideShaker export options? You can find them under the "Export > Identification Features" option in the PeptideShaker main menu at the top left. If none of the default reports fit your needs you can try making your own by clicking the "Add new report type" at the bottom left. Most of the features you need should be under the "Peptide Spectrum Matching Summary" category. You will probably have to calculate the delta score yourself though.
Hello,
I have matched a spectrum database to a target database with Search GUI and have loaded the results into Peptide Shaker with no issue
I need to export the results as a flat text file to later load into R but I'm having issues with the formatting. I need the ID, mass charge, sequence, score, length and Delta Score (difference between rank 1 and rank 2). I'm running it from the Desktop but I can't seem to find the option to even export the rank 1 PSM? A pep.xml file would work too. Thanks!