At Creative Proteomics, we specialize in integrated analysis of immunopeptidomics. Our platform offers comprehensive services that encompass the latest techniques and instrumentation to deliver in-depth insights into the immunopeptidome, aiding in advancing research, drug development, and personalized medicine. Integrated analysis of immunopeptidomics combines various cutting-edge techniques to provide a holistic view of the peptide repertoire presented by MHC molecules, enabling the elucidation of complex immune processes and the discovery of potential therapeutic targets.
What is Integrated Analysis of Immunopeptidomics?
Integrated analysis of immunopeptidomics is a scientific approach that combines different techniques and methodologies to comprehensively study the presentation and processing of immunogenic peptides by major histocompatibility complex (MHC) molecules. It involves the integration of mass spectrometry-based proteomics, bioinformatics, and immunology to understand the landscape of peptides presented by MHC molecules on the cell surface. Integrated analysis of immunopeptidomics encompasses several steps, including the isolation and purification of MHC-peptide complexes from cells or tissues, mass spectrometry analysis for peptide identification, and subsequent data analysis using bioinformatics tools. This analysis allows researchers to identify the source proteins from which the presented peptides are derived, predict peptide-MHC binding affinity, and study the immunogenic potential of these peptides.
Integrated Analysis of Immunopeptidomics by Creative Proteomics
- Identification of MHC-binding Peptides
Our team offers in-depth bioinformatics analysis to anticipate and assess the binding affinity between MHC molecules and peptides.
- HLA Peptidomics Analysis
Our services encompass a thorough analysis of HLA peptides to identify and characterize their constitution in specific individuals. Through implementing cutting-edge methodologies, we ascertain the distinctive repertoire of HLA peptides.
- Peptidomics-Based Antigen Discovery and Prediction
We offer comprehensive studies to investigate the interaction between peptides and antigens. Through techniques such as ELISA, surface plasmon resonance (SPR), or molecular docking simulations, we can assess the binding affinity and specificity of the identified peptides towards specific antigens.
- Immunopeptide Affinity Screening
- Screening of large peptide libraries against target antigens to identify high-affinity immunopeptides.
- Selection and validation of immunopeptides with optimal binding affinity and specificity.
- Tailored screening strategies based on project requirements and objectives.
- Comprehensive analysis of screening results and peptide ranking.
- Immune Peptide Library Screening
- Customized design and construction of immune peptide libraries tailored to specific research goals.
- Incorporation of diverse peptide sequences to maximize coverage of the peptide space.
- Strategic selection of peptide lengths and modifications to enhance library performance.
- Large-Scale Immune Peptide Mass Spectrometry Analysis
- Implementation of innovative mass spectrometry-based approaches, such as tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ).
- Integration of database searching algorithms and statistical tools for peptide analysis and interpretation.
Process of Integrated Analysis of Immunopeptidomics
The integrated analysis of immunopeptidomics involves a comprehensive approach to studying the major histocompatibility complex (MHC)-bound peptides and their interactions with the immune system.
- Sample collection
This process begins with the collection of biological samples such as tissue, blood, or cells, depending on the specific research question.
- Peptide extraction and purification
Following sample collection, peptides are extracted from the MHC complexes and purified. Various extraction and purification methods can be used, including affinity chromatography or immunoprecipitation techniques.
- Mass spectrometry analysis
The purified peptides are then subjected to mass spectrometry analysis.
- MHC binding prediction
In parallel, computational algorithms are used to predict the binding affinity of identified peptides to MHC molecules. This helps in understanding which peptides are likely to be presented by specific MHC alleles.
- Integration with Transcriptomics and Proteomics Data
The immunopeptidomic data is integrated with transcriptomic and proteomic data obtained from the same or related samples.
- Functional analysis
The identified peptides are further analyzed for their potential biological functions, such as their role in antigen presentation, interaction with T cell receptors, and immune response modulation.
- Validation
Selected peptides or their presenting MHC molecules are validated experimentally, often using techniques such as peptide-MHC binding assays or T cell activation assays.
- Biological interpretation
The final step involves interpreting the integrated data to gain insights into immune responses, such as antigen presentation, T cell recognition, and potential implications for diseases such as cancer, autoimmune disorders, and infections.
Techniques and Instrumentation for Integrated Analysis of Immunopeptidomics
- Mass spectrometry (MS): This technique is the foundation of immunopeptidomics and is used for the identification and quantification of peptides.
- Orbitrap mass spectrometer
- Quadrupole-TOF mass spectrometer
- Time-of-Flight (TOF) mass spectrometer
- Liquid chromatography (LC): LC is often coupled with MS to separate and analyze complex peptide mixtures. Different LC systems used in immunopeptidomics:
- High-performance liquid chromatography (HPLC)
- Ultra-high-pressure liquid chromatography (UHPLC)
- Nano-liquid chromatography (nanoLC)
- Tandem mass spectrometry (MS/MS): MS/MS is used to fragment peptides and obtain sequence information.
- Collision-induced dissociation (CID)
- Higher-energy collisional dissociation (HCD)
- Electron transfer dissociation (ETD)
- Electron capture dissociation (ECD)
- Peptide separation techniques: Various separation techniques are employed to reduce the sample complexity before MS analysis.
- Reversed-phase liquid chromatography (RPLC)
- Strong cation exchange chromatography (SCX)
- Isoelectric focusing (IEF)
- Next-generation sequencing (NGS)
NGS technologies are employed to sequence the MHC class I and class II peptide repertoires. This provides a comprehensive view of the entire set of peptides presented on MHC molecules.
Sample Requirements
- Experimental samples will not be returned, please back them up by yourself.
- Before sampling, a control group and an experimental group should be set up, and it is recommended to repeat more than 3 times for each group.
- There is no limit to the variety of peptides.
- For special requirements, please contact our staff for more information.
Due to the different types of samples, the sample volume and requirements for transportation conditions of each test item are also different. If necessary, please feel free to contact us.
* For research use only. Not for use in diagnostic procedures!
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