NYEPLAK

ProtVista Visualize all the protein information! As we continue to pile new genome and protein sequences into all these databases we have to come up with something better than just text sequences. You could argue that the few graphical sequence tools out there could use a refresh as well. Im happy to see that people are actively working on this stuff! Proof is in this extremely short open access paper in Bioinformatics! It details this new visualization tool, what resources it uses, where to download it and the source code but the coolest info in the paper (to me, anyway!) is that it is already in use by multiple tools we all already use! To verify I went after a protein I studied for a while, typed it into Uniprot -- and BOOM! Once you find the protein (and correct species) click the accession ID then click Feature Viewer and you get the ProtVista results! This isnt just colorful, its super useful. For example, if you click on PTMs, it expands and you get all these little symbols Hove...

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

PTMOracle Visualize PTMs !!! in Protein Protein Interaction data!! I dont have proof yet that this is as good as I think it might be. If it is, this is a serious missing link in proteomics filled in (courtesy of free software!!!) What I might be ridiculously excited about is the PTMOracle, which you can read about in this new JPR paper here. If you start doing any kind of PTM study and want to move to downstream analysis you will quickly find you need to: 1) Hijack some genomics tools built years ago for microarrays 2) Use some genomics tools someone hijacked years ago for microarrays and made kinda good at proteomics (and available) 3) Do lots and lots of manual work Those genomics tools are awesome. They really are. On the downstream analysis/data processing end, theyve got a 10 year head start on us. But -- upregulation of the entire ERK protein may do something very different in a cell than ERK phosphorylation on the normal active tyrosine (or the less common, biologically, but eas...