Proteomics analysis of 2013 Oscar Time Course Nitrate only Study

Version 2

Oscar time course was carried out between 8/19/2013 (Day 7) to 9/9/2013 (Day 28). This is a nitrate only study. Oscar time course samples were received from Jesse Cole. Proteomics sample preparation were done by Marina Gritsenko.

The Excel file contains multiple spreadsheets. It contains a summary of spectral count from all time points and proteins identified in each time point. Each time point has three biological replicates (A B, C). Each biological sample is sum of two technical LC-MS runs (data not shown).

Peptide spectrum matches were identified using MSGF+. The database was Hot_Lake_v3_UCC_Oscr_20150513_2015-05-27.fasta. Protein FDR calculation and protein assembly were performed using IDPicker. IDPicker filtered peptide identifications to < 1% 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.

Here I briefly explain the terminology in the spreadsheet. Some proteins are supported by exactly the same set of peptides, when this happens, instead of ditching those proteins, we assign these ambiguous proteins into distinct Protein Groups. Therefore, you might find two or three more proteins having same "Protein Group ID." 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.