Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass.
Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top-Down Proteomics provide a decision tree that guides researchers to robust protocols for mass analysis of intact proteins antibodies, membrane proteins and others from mixtures of varying complexity.
We also present cross-platform analytical benchmarks using a protein standard sample, to allow users to gauge their proficiency. These proteoforms can have different effects on important biological processes, including gene regulation, cell signaling and protein activity; consequently, the ability to characterize these species is essential for an understanding of the biological response to disease.
The identity of a proteoform can often be inferred 2 from an accurate experimentally determined intact mass 3. One can increase the sensitivity of intact-mass-based proteoform identification by determining the relative abundance of a particular amino acid by using isotopic labeling, by using mass similarities to cluster proteoforms into gene families and by reducing the search space using sample-specific search databases 2.
Localizing PTMs, and in some cases the definitive proteoform identifier, requires tandem mass spectrometry MS n analysis. Top-down MS protocols, unlike widely used bottom-up protocols 13 , 14 , do not require endoproteinase digestion before analysis, do not conflate proteoforms and tend to complement native MS analysis.
