FragIt roadmap

Translate the below points into actionable work packages; add detailed descriptions of each work package to issue board

• Use MSFragger
 to call peptides and modifications
  • Create container based on installation at Alex Schmidt's lab
• Download raw data via PRIDE's REST API
  • Write client to get data or use available one
• Prepare protein database for search
  • Download Uniprot set in FASTA format
  • Download reference transcriptome
  • Predict novel peptides from uORFs and potential translational readthroughs (up to lys/arg cleavage sites upstream)
  • Extend Uniport peptide set with predicted peptides
• Call MSFregger on input samples and extended peptide set and collect output
• Data analysis
  • Number of proteins identified per sample
  • Distribution of spectral counts per protein per sample
  • Principal component analysis of count data
  • Identification of sample-diagnostic proteins
  • Sample-specific expression of ribosomal proteins