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

Further developed, refined, and optimized since the original report of a routine multi-dimensional separation of protein species (most often using isoelectric focusing and then SDS-PAGE), and subsequently coupled with western blotting and MS, this approach was the first to identify the range of protein species/proteoforms in a variety of samples. Currently, the iTDP analytical approach offers the highest proteoform resolution and a routine approach to full proteome analysis (e.g., across the full breadth of species in native proteomes). In the case of 2D-PAGE, spots and/or regions of interest can be excised from the gel, proteolytically digested using well-established methods, and the resulting peptides then assessed using LC/MS/MS to identify canonical amino acid sequences and their inherent PTM (i.e. an 'integration' with BUP). Integration of this sequence information with the isoelectric point (pI) and molecular weight (MW) information from 2DE thus enables definitive identification of proteoforms based on several key defining physico-chemical characteristics. In addition to highly sensitive and quantitative total proteoform detection using fluorescent stains^[20]. and notably Coomassie Brilliant Blue as a near-IR dye, gel staining protocols also enable the identification of broad proteoform groups containing the same PTM (e.g. phospho- and glyco-proteoforms). Thus, iTDP utilizes integration of the best available approaches to enable truly comprehensive, deep proteome analyses at the critically necessary level of proteoforms. Accordingly, following critical evaluation to ensure comprehensive, quantitative analysis, new approaches can also be integrated once fully vetted (see below).

MSi-TDP (sometimes referred to as TD-MS) is a method of proteoform identification that uses a mass spectrometer to determine the mass of a species from the charge series of the resulting ions and obtain sequence information by selecting a single charge state ion for MS/MS analysis . The stated goal of MSi-TDP is to carry out proteoform analysis fully in the mass spectrometer using a variety of fragmentation methods (e.g. collision-induced dissociation, electron-capture dissociation or electron-transfer dissociation).  Due to proteoform molecules taking up different numbers of H+ ions and forming multiple charge states, having multiple different proteoforms appearing in the mass spectrometer at the same time can create extremely complicated spectra that are difficult to deconvolute and analyse, while also having the potential for ion suppression that reduces signal and sensitivity. This is most effectively overcome by separating the different proteoforms, typically by tube gel electrophoresis and subsequent reversed phase chromatography, immediately prior to ionisation, to reduce the number of proteoforms entering the instrument at a particular moment. Therefore, like iTDP, effective sample/proteome fractionation is critical before MSi-TDP to ensure success of analyses within the limitations of the method. Thus, in contrast to BUP, MSi-TDP interrogates proteoform structure through measurement of an intact mass followed by direct ion dissociation in the gas phase. A second challenge concerns the sequence coverage that turns lower for larger proteoforms as a result of less backbone fragmentation, thus affecting the confidence of the identifications.

The definition of TDP includes a requirement to identify the "protein", either as a distinct proteoform or ORF product. While this is most typically achieved using a mass spectrometer to fragment ions, from either intact proteoforms or peptides of resolved proteoforms, it is also possible to identify and quantify canonical "proteins" using affinity-based reagents, such as O-link and SomaScan which use antibodies or aptamers, respectively. The generic term "protein" is used here because it is unclear whether these reagents identify certain proteoforms or a variety of proteoforms from the same ORF product. These methods thus produce similar, yet different, information relative to each other and to proteogenomic BUP approaches using LC/MS/MS. Because of the claimed (i) "depth" of these assays in terms of identifying canonical protein sequences; and (ii) apparent ability to quantify changes in the abundance of those proteins in samples that can be problematic for other proteomics technologies (e.g.  plasma and serum), these technologies have become popular in studies having enormous sample numbers that are impossible to directly address by other proteomics technologies. However, the substantial lack of correlation between these technologies, as well as with other established proteomics technologies, needs to be addressed, along with fully characterizing the exact proteoforms that these reagents are identifying. This will thus also require transparent verification of the quality and selectivity of any antibodies and aptamers used. Expense must also be duly considered with such assays as they become more frequently applied in very large studies (e.g. potentially involving thousands of samples).