mammalian-bacterial, honeybee-bacterial, honeybee-mite.
Our lab is focused on quantitative proteomics using LC-ESI-MS to study biological systems. We cover a wide range of topics including pathogen invasion, infection, protein localization, and mapping protein interaction.
Mass spectrometry-based proteomics:
In order to understand how a complex system works it is extremely useful to know the identities of as many of the components of the system as possible. Commercially available mass spectrometers and database search tools have advanced to the point where experienced laboratories can routinely and reliably identify hundreds or thousands of proteins in exceedingly complex mixtures (i.e. an organelle preparation) using nanoflow high performance liquid chromatography (HPLC)/tandem mass spectrometry (LC/MS). Typically, complex protein samples are reduced to peptides by highly specific enzymatic digestion (e.g. trypsin cleavage carboxy-terminal of Arg or Lys). The peptides are then resolved by extremely high-resolution reversed-phase chromatography and eluted/ionized directly into a mass spectrometer (MS). The MS, operating in an information-dependent mode, selects and isolates any peptide ions observed and subjects them to tandem mass spectrometry. The observed mass/charge ratio of the peptide and its fragmentation pattern are then used to scan comprehensive protein sequence libraries (e.g. for a human liver sample the data would be searched against the Homo sapiens library) to find the best theoretical match and the peptides are compiled to arrive at a ‘protein hit list’.
In the past few years we have witnessed great advances in methodologies for applying mass spectrometry-based proteomics to answer biologically relevant questions. Some of the most powerful of these methods involve the use of stable isotopes to incorporate a quantitative dimension into the experiment. Thus far, however, quantitative proteomics has yet to be widely applied in mainstream biology. Our group is interested in a multidisciplinary approach to relevant cell biological problems. We develop and apply quantitative proteomic methods to questions involving organelles and how the composition of these compartments change when antagonized. Additionally, we are involved in several projects involving host-pathogen interactions. The knowledge gained from proteomic experiments is then used to direct more in-depth biochemical, bioinformatic and cell biological analysis of the system in order to validate the proteomic results. We have an LTQ-Orbitrap and an LTQ-FT in our laboratory, both equipped with autosamplers and nESI-interfaced HPLCs.
Finding host targets of effector proteins secreted from pathogenic bacteria
Protein interaction network mapping of methicillin-resistant S. aureus (part of the PRoteomics for Emerging Pathogen REsponse
Exploring why young honeybee larvae are susceptible to invading bacteria, especially to Paenibacillus larvae , the causative agent of American Foulbrood.
Exploring the dynamic composition of lipid rafts
Host signal transduction cascades initiated by pathogens
Host receptors for pathogenic bacteria
Development of software tools to improve the acquisition, analysis, storage and dissemination of proteomic data
- McAfee, A., H. Higo, R. Underwood, J. Milone, L.J. Foster*, M.M. Guarna*, D.R. Tarpy* and J.S Pettis*. “Queen honey bees combat heat stress-induced loss of stored sperm viability with ATP-independent heat shock proteins.” NATURE SUSTAINABILITY. 3 (2020): 367 – 376.
- Kerr, C.H., M.A. Skinnider, A.M. Madero, D.T. Andrews, R.G. Stacey, Q.W.T. Chan, N. Stoynov, E. Jan and L.J. Foster. “Dynamic rewiring of the human interactome by interferon signaling.” GENOME BIOLOGY. 21.1 (2020): 140. doi: 10.1186/s13059-020-02050-y. PMID 32539747.
- Stacey, R.G., M.A. Skinnider and L.J. Foster. “On the robustness of graph-based clustering to random network alterations.” MOLECULAR & CELLULAR PROTEOMICS. 20 (2021): 100002. doi: 10.1074/mcp.RA120.002275. PMID 33148787.
- McAfee, A., A. Chapman, J.S. Pettis, L.J. Foster and D.R. Tarpy. “Trade-offs between sperm viability and immune protein expression in honey bee queens (Apis mellifera).” COMMUNICATIONS BIOLOGY. 4.1 (2021): 48. doi: 10.1038/s42003-020-01586-w. PMID 33420325.
- Skinnider, M.A., N.E. Scott, A. Prudova, N. Stoynov, R.G., Stacey, Chan, Q.W.T., Rattray, D., J. Gsponer* and L.J. Foster*. “An atlas of protein-protein interactions across mammalian tissues.” CELL. 184.15 (2021): 4073-4089.e17. PMID 34214469. doi: 10.1016/j.cell.2021.06.003.