Finding a vocation for validation: taking proteomics beyond association and location

Abstract

First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision-making processes. With ever-growing...

Precision Immuno-Chemical Biology: Toward Decoding Spatiotemporal Signaling Activities of Reactive Immunometabolites

“…The limited quantity of electrophile transiently made available within the designated Halo locale, is competed by native electrophile-sensor proteins proximal to Halo. Coupling this electrophile function-guided proximity-mapping platform (Localis-REX) to enrichment-proteomics workflows [90] enables quantitative target-ID/ranking among kineticallyprivileged local responders. A recent example of Localis-REX demonstrates nucleus-vs. mitochondrial outermembrane-specific precision localized delivery of lipid-derived signaling electrophiles (LDEs) [91].…”

Let’s Get Biophysical – How to Get Your Favorite Protein’s Digits

“…However, TMT can nowadays be carried out in 11 or more multiplex, whereas, for instance, in-cell/in-vivo mass tagging through stable isotope labeling of amino acids in cell culture (SILAC), can only be used in triplicate. For readers interested to delve deeper into MS proteomics capabilities and for chemical biological or biochemical investigations, we refer them to our recent mini-review [1]. With the improvement of modern MS methods, it is now quite common to use label free quantification (LFQ) MS, which compares ion signatures per run in native digest samples.…”

“…As the method is particularly sensitive to nuclear environment, in an NMR spectrum, non-equivalent nuclei within a sample show up as specific peaks, each of which have a defined value, referred to as a chemical shift. In standard protein NMR measurements, 1 H and 15 N are used in a two-dimensional experiment, to separate out peaks that would otherwise be occluded in one-dimensional experiment. In this experiment broadly known as heteronuclear single quantum coefficient (HSQC), N-H bonds show up as specific peaks in a two-dimensional grid.…”