Re analysis of the great Gomez Baena et al dataset They arent messing around!
Re analysis of the great Gomez Baena et al dataset They arent messing around! Yesterday I made a short post on this new study in Open Reports. Ill be honest, I thought it was a seriously impressive sample set, but I was a little skeptical about the results. Not that I didnt believe the authors could find the bacterial proteins, but I was skeptical that the results could be that clean cut. Ive seen a few "identification of digested bacterial proteins in body fluid" studies and even with high resolution data the matrix is complex enough that there is noise there. These results just seemed a little too good to be true. Shoutout to ProteomeXchange/PRIDE and these authors for making this data extremely easy to obtain, sort and reprocess overnight!! For my re-analysis, I threw all the files into PD 2.2 and used the default processing workflow for LTQ-Orbitrap LFQ and LFQ concensus with enhanced annotation. I made a 77MB FASTA in PD by parsing a UniProt TrembL I downloaded in July...