Data Master Thesis: Managing Spectral Library Search Space with Deep Learning for Protein Modification Site Discovery in DIA Proteomics

results.zip├── Orbitrap AIF│ ├── diann│ │ └── raw search engine outputs│ └── alphadia│ └── raw search engine outputs ├── TTOF6600 SWATH│ ├── diann│ │ └── raw search engine outputs│ └── alphadia│ └── raw search engine outputs├── TimsTOF Pasef│ └── diann│ └── raw search engine outputs (with XICs)│ └── Orbitrap Exploris 480 ├── diann │ └── raw search engine outputs └── alphadia └── raw search engine outputsdata.zip├── proteome fasta files├── phospholingo models training data├── phospholingo predictions used to make the spectral libraries└── phosphosite-plus literature data