LipiDex Spectrum Annotator

C# script to annotate LipiDex spectral matches from PeakFinder and Spectrum Searcher modules

File structure

LipiDex search results, spectral data in MGF format, and libraries must be stored in this directory layout for this script to work correctly. Refer to the example folder structure section of this repository for a quick copy-paste solution. Spectral data and Spectrum Searcher results need to be a in a 1-1 relationship, meaning for every file you processed in LipiDex, there must be a resulting MGF, Spectrum Searcher .csv, and be in the AssociatedSpectra.csv table. Missing files shouldn't cause any problems, but extra files will cause the script to crash.

Base Directory (Name of this one not important)
├── Annotated Spectra
    └── Contains the generated annotated spectra as PDFs
├── Associated Spectra
    └── The AssociatedSpectra.csv table generated by Peak Finder
├── LipiDex Msp Files
    └── The .msp format libraries used to search your lipid data.
├── MGFs
    └── Spectral data.
└── Spectrum Searcher
    └── The .csv output from the Spectrum Searcher module for each file you want annotated.