[getoffmycase]

I disagree. I think that proteomics is useful without spatial information because it captures a snapshot of cell state, or tissue state rather, of signaling networks via PTMs along with abundance measurements. If you don’t have spatial orientation, you at least have temporal information.

I think increasing the yield of MS2 scans to PSMs specifically by dealing with spectra containing PTMs and chimeric spectra will further enable deeper understanding of cell signaling. Additionally, the targeted analysis of specific sub-proteomes using real time search, using GoDig from the Gygi lab for example, also seems very promising.

Plus, there’s large industry efforts using proteomics as a drug screening tool, an application that doesn’t require spatial resolution of anything. Specifically groups are looking for protein expression knockdown, but it’s not too far a stretch to look for pathway perturbations using real time search and careful controls.