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...