home.md

+# FragIt roadmap
+
+> Translate the below points into actionable work packages; add detailed descriptions of each work package to issue board
+
+* Use [MSFragger](http://msfragger.nesvilab.org/)
 to call peptides and modifications
+  * Create container based on installation at Alex Schmidt's lab
+* Download raw data via [PRIDE's REST API](https://www.ebi.ac.uk/pride/ws/archive/#!/peptide)
+  * Write client to get data or [use available one](https://www.ebi.ac.uk/pride/help/archive/access/webservice)
+* 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
+