Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics?

Over
the past 40 years, proteomics, generically defined as the
field dedicated to the identification and analysis of proteins, has
tremendously gained in popularity and potency through advancements
in genome sequencing, separative techniques, mass spectrometry, and
bioinformatics algorithms. As a consequence, its scope of application
has gradually enlarged and diversified to meet specialized topical
biomedical subjects. Although the tryptic bottom-up approach is widely
regarded as the gold standard for rapid screening of complex samples,
its application for precise and confident mapping of protein modifications
is often hindered due to partial sequence coverage, poor redundancy
in indicative peptides, and lack of method flexibility. We here show
how the synergic and time-limited action of a properly diluted mix
of multiple enzymes can be exploited in a versatile yet straightforward
protocol to alleviate present-day drawbacks. Merging bottom-up and
middle-down ideologies, our results highlight broad assemblies of
overlapping peptides that enable refined and reliable characterizations
of proteins, including variant identification, and their carried modifications,
including post-translational modifications, truncations, and cleavages.
Beyond this boost in performance, our methodology also offers efficient de novo sequencing capabilities, in view of which we here
present a dedicated custom assembly algorithm.