NYEPLAK

Quantitative multiplexed protocol for biomarker discovery EDIT (5 min after posting and remembering I forgot something that seemed somewhat important...): The subtitle of this paper should be -- HOW TO RELIABLY QUANTIFY 4,000 PROTEINS IN HUMAN PLASMA ! I dont have time this morning to read this whole new Nature Protocols paper as its quite large (19 pages) and Im going to argue that its really several protocols -- but it looks like a seriously valuable resource to me! What I can tell you: 1) Its exceptionally well-written and clear -- and thorough 2) It shows outstanding reproducibility with isobaric tags -- despite the use of abundant protein depletion (which I generally consider to be something that negatively impacts reproducibility) 3)The troubleshooting section is AWESOME. I suspect at least one of these authors has trained people on these protocols in their facility a few times. I stored this away to refer to later -- and to send to anyone thinking about doing reporter ion quan b...

Quantitative assessment of digestion techniques for protein protein interactions! This new study ASAP at JPR is an incredibly thorough (QUANTITATIVE!) analysis of different pull down and digestion techniques for Protein-Protein Interaction (PPI) experiments. Honestly, Im filing it away as a reference for the next time I try to do one of these. This thing is a textbook of how to optimize a PPI experiment. Of course, this isnt the first one of these weve seen, but rather than doing PSM counts or even # of peptide/proteins IDed, this study does LFQ with MaxQuant (quadrupole Orbitrap) and then use stable isotope SRM quantification. An interesting observation is that higher abundance proteins are easily quantifiable just about regardless of the pull-down and digestion methods. To get to the lower abundance things, they really need to fine tune the methodology. download  file  now