Top-down proteomics
Top-down proteomics is a method of protein identification capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry, intact proteoforms are typically ionized by electrospray ionization and analysed using a variety of mass analysers, including Orbitraps, Ion Cyclotrons and Time-Of-Flight. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Typical proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS; Bottom Up proteomics). Top-down proteomics using mass spectrometry interrogates protein structure through measurement of a proteoform's intact mass followed by direct ion dissociation in the gas phase. Top Down proteoform analysis can also be achieved through resolution (separation) of the proteoform from all other proteoforms and then applying peptide-centric LC-MS/MS to characterise the isolated proteoform.
A single gene can be coded for many protein products (e.g. via alternative splicing; post-transcriptional and -translational processing) and the resulting canonical amino acid sequences (i.e. 'proteins' or more correctly Open Reading Frame (ORF) products) can be further modified by any number of post-translational modifications (PTM) or non-physiological adducts. These varied protein species or proteoforms define proteomes and are the functional entities underlying biological processes. Thus, truly comprehensive or 'deep' proteome analyses must assess proteoforms.
There are two general approaches to proteome analysis - bottom up (BUP or shotgun) and top down (TDP). The former, a peptide-centric or proteogenomic approach, infers (often with quite limited data) the identities of canonical protein sequences by correlation with existing databases, mostly derived from genome sequencing projects. In contrast, TDP can, in theory, yield comprehensive proteome analyses at the level of proteoforms provided the methods used effectively address the full breadth of species in a proteome.
Adopted from analytical chemistry, the term top down in proteomics means the separation of intact proteoforms and their subsequent identification, and is agnostic as to how that is achieved. Currently, there are two analytical approaches that enable proteome assessments to different extents: Integrative or Integrated TDP (iTDP; current usually utilizing routine high resolution/sensitivity two-dimensional gel electrophoresis tightly coupled with liquid chromatography and tandem mass spectrometry (2DE/LC/MS/MS)) or mass spectrometry-intensive TDP (MSi-TDP); while these terms may not yet be widely used, it is important to differentiate between these approaches as they enable quite different depths and comprehensiveness of proteome analysis. Such clear distinction is critical in terms of the transparency, accuracy, and thoroughness of proteome research. As always, it is critical for every study to fully describe the methods used.
Thus, although currently most often utilizing 2DE/LC/MS/MS, iTDP is a more general term for the integration of the best available approaches to enable truly comprehensive, deep proteome analyses at the critically necessary level of intact proteoforms. Accordingly, following critical evaluation to ensure comprehensive, quantitative analysis, new approaches can also be integrated as the critical front-end of analysis once fully vetted for their ability to resolve a full breadth of intact proteoforms inherent to proteomes, as can a variety of proteases and LC/MS/MS adaptations to ensure the highest quality peptide analyses and thus proteoform identifications