Grant applications proposing work that will be performed by Protein Sciences or with Protein Sciences’ assistance do not require letters of support unless the methods that will be used are not included in Protein Sciences’ service description in the JAX Facilities and Other Resources master document (see description below). For methods that are unusual or particularly challenging, or that were recently published, please discuss with the Protein Sciences Director whether a letter of support would be appropriate.
Given the custom nature of each investigator’s project, please contact us to discuss service pricing.
Protein Sciences (PS) provides services and expertise related to mass spectrometry characterization of proteins, small molecules and lipids, the generation and validation of antibodies, and production/isolation/characterization of proteins. For each of these areas, PS also offers consultation and training on experimental design, selection of methods, custom method development, and data analysis, as well as interpretation and presentation of results. To carry out this spectrum of services, PS comprises two service groups working together to meet the needs of internal and external investigators.
The Mass Spectrometry and Protein Chemistry Service (MSPC) provides expertise and high-throughput analyses for proteomics, metabolomics, and lipidomics, as well as targeted studies for each of these methods of analysis. Preparation of protein and metabolite samples (performed in an attached BSL-2 sample preparation lab), appropriate liquid chromatography–mass spectrometry analysis, mass spectrometry imaging, and data analysis are offered. Complete proteomics and metabolomics analysis pipelines are available for both qualitative and quantitative analysis. Staff scientists and technical personnel in the MSPC have over fifty years of combined experience in protein science and thirty years with mass spectrometry-based technologies. Drawing from this experience, the MSPC also offers their expertise for troubleshooting protein, metabolite, or lipid projects as needed and/or develops custom methodology for investigators.
The MSPC has instrumentation for bottom-up proteomics, intact protein determination, data-dependent and -independent acquisition, and specific post-translational modification analysis. Qualitative and quantitative analyses are available as determined by the project’s needs. The proteomics analysis pipeline is primarily based on Proteome Discoverer™ with nodes for Chimerys, Mascot, Sequest™, Comet, and MSfragger in the service. Proteomics on the Bruker Ultra 2 mass spectrometry system is supported by the ProteoScape analysis software containing Spectronaut 19. The MSPC offers two metabolomics analysis pipelines: targeted and discovery. The metabolomics platform enables targeted quantitation of select pathways and is supported by the MzCloud, HMDB, and Metlin metabolite/lipid databases, in addition to custom-designed metabolite databases in house, that allow for high-confidence identification. The discovery metabolomics platform provides analysis of up to four different combinations of chromatography and mass spectrometry detection. These metabolomics pipelines are supported by Mass Profiler Professional, Compound Discoverer, TraceFinder, FreeStyle, MetaboAnalyst, and XCMS software. The MSPC also has a Bruker timsTOF fleX mass spectrometer in the facility, bringing mass spectrometry imaging at high spatial and mass resolution, as well as the ion mobility benefits of the Trapped Ion Mobility for both ESI and MALDI. This feature provides additional characteristic parameters of collisional cross-section for metabolite and peptide identification. This system comes with PaSER for real-time searching of proteomics data. MetaboScape is also available for metabolomics data on the timsTOF fleX. SCiLS Lab and timsViewer integration with MetaboScape is utilized for analysis of mass spectrometry imaging data collected on the timsTOF flex.
The Monoclonal Antibody and Protein Production Service (MAPP) has two main laboratory focus areas, 1) monoclonal antibody generation and validation and 2) protein production and purification, as described below. MAPP facilities include BSL-1 and BSL-2 space.
The Monoclonal Antibody laboratory produces new monoclonal antibodies against protein or peptide targets using classical hybridoma technology supported by high-throughput methods, as well as scale-up production of antibodies from existing hybridoma cell lines. Advice and consultation on immunogen design and peptide selection are provided using a suite of software. This includes 3D structural modeling and analysis of proteins to select optimal immunogenic peptide sequences; analysis of biophysical properties of selected candidate peptides; and advice on carrier protein selection and purity of reagents required. The custom monoclonal antibody service includes quality-control testing of incoming immunogens; processing of ethical approval requirements; selection of suitable adjuvants and preparation of immunization samples; immunization of mice with samples; collecting serum from mice and determining antibody titer by ELISA; harvesting immune tissues; creation of hybridoma cell lines using robotics; screening of hybridoma immunoreactivity using ELISA; secondary screening by antigen-specific ELISA and western blot; tertiary screening, kinetics, and epitope binning using multiplex surface plasmon resonance (SPR) and biolayer interferometry (BLI) assays; production of test samples of antibodies; cryopreservation of cell lines; subcloning of cell lines to monoclonality; and determination of antibody isotypes. Scale-up production is also provided with the capacity to produce multi-milligram quantities of purified antibody. Antibody purification utilizes protein A or protein G columns or affinity purification via antigen-coupled resin columns.
The Protein Production laboratory designs and constructs expression vectors, utilizes bacterial and human HEK293 cell line expression systems, and purifies proteins of interest by biochemical fractionation using a wide spectrum of chromatographic columns that exploit protein size, physical properties, and fused protein tags. All isolated proteins are quality-control-checked for purity and contaminants by mass spectrometry and SDS-PAGE. Additionally, the service performs gel electrophoresis and traditional western blot analyses.
If you have used any of JAX’s Scientific Services, please acknowledge the Service(s) used in all manuscripts, publications, grant applications, press releases, and presentations. Example language for the use of the Protein Sciences Service is below:
“We gratefully acknowledge the (Mass Spectrometry and Protein Chemistry Service or the Monoclonal Antibody and Protein Production Service) within Protein Sciences at The Jackson Laboratory for their contributions to this study.”