Oscar and Ana Exoproteome 2013 Pilot

Version 1

This is the first attempt to characterize proteins in the supernatant in Ana and Oscar. Oscar was harvested 10/08/2013 representing Day 14 (By Jesse Cole). Ana was harvested on 12/26/2013 representing Day 21. Supernatant was collected by passing though 0.2 um filter. Proteomics analysis was carried out using online trypsin digestion cart to increase sensitivity and reduce sample loss.

Peptide spectrum matches were identified using MSGF+. The database was Hot_Lake_v3_UCC_Oscr_20150513_2015-05-27.fasta and Hot_Lake_v3_UCC_Ana_20150513_2015-05-27.fasta. Protein FDR calculation and protein assembly were performed using IDPicker. IDPicker filtered peptide identifications to < 3% Protein FDR using decoy database matches, built a bipartite graph of peptide–protein relationships, and assembled a list of protein identifications through a parsimony reduction of the bipartite graph.

Brief explanation of the terminology in the spreadsheet: Some proteins are supported by exactly the same set of peptides, when this happens, instead of getting rid those proteins, we assign these ambiguous proteins into distinct Protein Groups. Therefore, you will find two or three more proteins sharing same "Protein Group" number. Other terminology includes "Distinct Peptide" which refers to distinct sequence of amino acids. "Filtered Spectra" refer to peptide spectrum matches.

P.S. Watch out for duplicated proteins.