Fixing Unmodified Protein sequences

Hotfix: Resolve issues with inputting unmodified protein sequence (Just leave column H - noncys mods empty to indicate unmodified). Added details to the manual. Fragariyo was able to handle unmodified fragments before, the problem was running initial unmodified proteins. No need to rerun modified protein runs.

Coordinate Agilent file Update

User do not have to add column name to the coordinate Agilent file anymore. Experimental ions needed by Input Generator section can be unmatched ions (this has been added to the dialog window).

Updated ion type definitions, output information, and batch mode

• Updated ion type definitions. User can now select CID or ECD (it will make sure the correct ion types are used). Other electron-based fragmentation chemistries will be added upon user request.
• For internal fragment searches, output now contains mass resolution used to generate theoretical isotope envelopes and tolerance error for matches.
• Batch mode is now available for internal fragments (several searches can be run automatically).

Updated Ion Types Definitions for z-ions

Masses for z-ions where 1 Da off , now it is fixed.
Message alerting that the column of charges (in experimental ion list) is in the wrong order was included (appears in the terminal window if the input file is not properly formatted).

Fixed Modifications hotfix

Problems parsing fixed modification residue number have been fixed

GUI Support

Fragariyo is a set of Python 3.7 scripts. Now with GUI-support it peak matches terminal fragments and internal fragments. The program was created using IMTBX/Grppr outputs, Agilent IMMSBroser .csv files, generic .csv files (m/z,z/int). The program can plot sequence coverage based on intensity or just sequence position. It can handle disulfide-bonds (user can input existing disulfide bonds and tell program how many to break). Let's hunt for fragments!

If there are issues with opening the GUI, got to C:\Program Files (x86)\fragmentor_build\ and rename the folder .ui to UI