NYEPLAK

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...

Reprocessing one of the Bekker Jensen et al datasets! Ummm....so....yesterday I was pretty psyched about the Bekker-Jensen et al., paper in Cell Systems. I pulled all the files from one cell line that I have a LOT of data on. Some Ive fractionated and ran myself. And Ive got nothing that has given me 75% of the PSM/peptide/protein IDs that this does. 33 min nanoLC runs?!? No way Im going to see over 12,000 unique human proteins at high confidence...No way.... I rechecked my setting to make sure I didnt do anything stupid and reran a fractionated dataset from the same cell line from a similar instrument to verify. Nope. This method is legit. Ive just been doing nanoLC the same way for todays super fast instruments that I was doing it for yesterdays not-as -super-fast instruments and inadvertently handicapping the potential they have for 2D fractionated samples! Important disclaimer in my numbers above -- I am using a supplemented FASTA that may be inflating my numbers to some degree (t...