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Top-down (Intact) Proteomics

Proteins are critical structural and functional components of biological organisms. A single gene may produce many different molecular forms of proteins via post-transcriptional, post-translational modifications or noncovalent complex formation with other molecules. New advances in mass-spectrometry-based proteomics have enabled direct analysis of intact proteins and native protein complexes. While the more conventional proteomics approaches study proteins “bottom-up” by measuring small peptide fragments, these techniques offer a “top-down” view of proteins at the intact level, allowing us to better understand their structures and functions.

instruments for Omics and Mass Spectrometry for Intact Proteins and Top-down Proteomics
EMSL has a variety of mass spectrometry resources for intact proteins and top-down proteomics to support the Structural Biology and Biomolecular Pathways Integrated Research Platforms.

Research application

  • Supporting the Structural Biology Integrated Research Platform, these resources can measure stoichiometry of protein-protein, protein-nucleic acid, protein-ligand, and protein-metal complexes. The information will help us better understand protein structure and function, including heterogenous and dynamic protein assemblies.
  • Supporting the Biomolecular Pathways Integrated Research Platform, these resources can precisely define “proteoforms” at the intact protein level—combinations of post-translational modifications and in vivo proteolytic cleavages.

Available instruments

  • Thermo Orbitrap UHMR
  • Waters Synapt G2s-I Ion Mobility Time-of-flight
  • Thermo Orbitrap Eclipse Tribrid
  • Thermo Orbitrap Fusion Lumos

Available software

  • IsoForma tool for automated quantification of isomeric proteoforms
  • PSpecteR application tool and R package for annotation of fragmentation patterns

Tips for success

  • Current technology is best suited for targeted analysis on enriched, purified, or recombinant protein samples. New technologies and instrumentation are also being actively developed for more complex samples; please contact your EMSL science point of contact for details.

Contacts