Top-Down, Bottom-Up

Early genome sequencing methodologies utilized top-down approach and is employed in further detailing of the structural characterization of nucleic acids, proteomics fields are being revolutionized through this approach to develop proteoform maps without information loss.

Biological systems generated by computational modeling are used in the systems biology field to determine the complex macromolecular interactions occurring within organisms. Models built to understand cell metabolic behaviour can be approached in opposite directions. Draft reconstruction of networks which can be simulated under varied physiological conditions is encompassed by the bottom-up approach. Collection of data on organism specific information is gathered into a genome scale model extracted through bioinformatic software tools, contrasting to top-down approach reconstructing metabolic networks from experimental data. Using the path of information moving from simulated metabolic pathways to transcriptome or proteome the underlying interactions become understood, gathered from data gained from common technology such as mass spectrometers and DNA microarrays.

Hierarchical shotgun sequencing uses top-down approach. Prior to being broken into fragments and then reassembled, low resolution maps of the entire genome is created, making it possible to form a series of overlapping fragments, that do not require sequence assembly algorithms, minimal numbers of fragments can than be chosen that span the entire chromosome. Hierarchical shotgun sequencing was replaced with whole genome shotgun sequencing as primary genome sequencing method in 2003.

Top-down approach to mass spectrometry can be seen in the analysis of intact biomolecules that are part of a larger greater complex, such as tandem mass spectrometry utilized for the DNA/RNA identification, that has an advantages over other biochemical analysis methods with the ability to determine modifications with increased sensitivity. Structural characterization of nucleic acids is provided by identified fragmented ions that can be utilized in future development of gene therapy. Increased understandings of modifications to nucleic acids that occur in nature, addition of groups are linked to stability changes and consequential changes in function, mapping fragmentation mechanisms of nucleic acid ions the underlying biomechanisms of stability changes can be understood and possibly utilized in modifications.

Proteomics fields are most commonly used top-down approach, with bottom-up mass spectrometry digesting proteins into peptides for identification, top-down proteomics introduces intact proteins to mass spectrometer measuring with both fragmented and entire ion masses. Gaining understanding of protein complexity proteoform mapping without information loss is important, risk of details such as sequence variants being lost on separate peptides is typically eliminated with use of top-down approach. Top-down mass spectrometry advances make mapping of larger proteome complexes available, having possible ramifications for development of future protein therapeutics, particularly in development of larger protein based drugs requiring tests as a whole in terms of molecular components.