What is Proteomics?

Proteomics is the study of the proteome, the entire set of proteins produced by a living system. It involves identification of proteins, investigation of protein abundances, the variations, and modifications therein, as well as insight into interacting partners and networks.

Practical applications of proteomics include

  • New drug discovery
  • Mechanism of action
  • Protein identification
  • Protein quantitation
  • Interaction Proteomics and Protein Networks
  • Expression Proteomics
  • Biomarkers
  • Proteogenomics

At Emery Pharma, we have a comprehensive platform with advanced instruments including UPLC-HR MS, GC-MS, UPLC-QqQ-MS/MS, and NMR that can be applied to the analysis of a single protein or used for the large-scale analysis of a proteome including protein abundances, modifications, protein-protein interactions, and protein-compound interactions.

Our proteomics services support cancer research, diagnostic biomarker discovery, microbiology, antibody profiling, and drug discovery and development. We are happy to support our clients with our deep expertise across the proteomics pipeline.

Bottom-up and Top-down Proteomics

Proteomics is usually performed using two different strategies: bottom-up and top-down approaches.

Bottom-Up Approach to Proteomics

In the bottom-up approach, a crude protein mixture is subjected to proteolytic cleavage, and the peptide products are analyzed by mass spectrometry.

This approach routinely allows greater sequence coverage, resolution of sequence ambiguities and preservation of post-translational modifications. Peptides are more easily separated by LC as compared to intact proteins, and ionize and fragment more efficiently in the MS, making it a robust methodology for high-throughput analysis for identification and quantification of complex proteins mixtures.

Top-Down Approach to Proteomics

In the top-down approach, intact proteins are characterized by mass spectrometry without prior proteolysis.

This approach offers the ability to study protein isoforms, sequence variants, as well as significantly simplifies the sample preparation, data analysis, and quantitation process. This method is superior for especially low mass protein detection since the inability to generate sufficient tryptic peptides can be challenging for MS analysis.

Emery Pharma offers extensive experience in both bottom-up and top-down proteomics. Please inquire to discuss your proteomics projects, matrix compatibility, and choosing the right workflow.

Emery Pharma is proud to offer the following Proteomics Services:

  1. Protein identification - Emery Pharma offer a comprehensive platform for protein identification pipeline, which involves sample preparation, chromatographic separation, mass determination, and systematic bioinformatics analysis. Both bottom-up and top-down approaches can be utilized, followed by mass spectrometry-based analysis.
  2. Protein quantitation - Emery Pharma provides quantitative and systematic evaluation of differences in protein profiles of distinct samples using stable isotope labeling (SIL) and label-free approaches. SIL approach allows detection of differences in protein abundance among samples using non-radioactive isotopic labeling. In this approach, a known concentration of isotopically labelled peptide(s) is spiked into the sample. The absolute quantitation of the target peptide is achieved based on MS intensity comparison with the isotopically labeled peptide(s). Label-free approach doesn’t require isotopically labelled standard and allows determination of relative abundance of proteins. Label-free quantitation may be based on precursor signal intensity or spectral counts. While this approach does not offer absolute quantitation, it still provides valuable comparative information. It can be more economical as it doesn’t require extensive labelling workflows, but still achieves high proteome coverage.
  3. Peptidomics - Peptidomics is a variation of traditional proteomics that involves qualitative and quantitative analysis of endogenous peptides from biological samples. Peptidomics workflow mimics bottom-up proteomics with modifications made to sample preparation and MS analysis based on the project’s needs.
  4. Protein post-translational modification (PTM) analysis - Identification of sites of post-translational modification is vital to fully understand biological roles of a protein. Post-translational modification (PTM) regulates activity, localization, and interaction with other cellular molecules such as proteins, nucleic acids, lipids, and cofactors. Emery Pharma provides an advanced analytical platform for the characterization of various PTMs.