Welcome to Creative Proteomics, the leading provider of advanced proteomics services. At Creative Proteomics, we offer comprehensive services for peptideomics functional annotation and enrichment analysis to provide valuable insights into the characteristics and functions of peptides.
What is Peptideomics Functional Annotation?
Peptide functional annotation is the act of elucidating and ascribing distinct functions or roles to peptides. Peptides, being brief sequences of amino acids, possess a range of biological functionalities within organisms. The process of functional annotation encompasses the delineation of biological activities, biochemical functions, and molecular interconnections attributed to specific peptides. This endeavor may be accomplished through diverse methodologies, including computational analysis, the utilization of bioinformatics tools, and empirical investigations. The overarching objective of peptide functional annotation lies in providing discernment into the implications, mechanisms, and prospective applications of peptides in various biological phenomena, encompassing the realms of signal transduction, regulatory processes, immune responses, and therapeutic interventions.
Peptideomics Functional Annotation and Enrichment Analysis by Creative Proteomics
- Functional Annotation
Using advanced bioinformatics tools and databases, we annotate identified peptides with functional information, including protein associations, gene ontology terms, pathway involvement, and protein-protein interaction networks.
- Enrichment Analysis
Our enrichment analysis focuses on identifying overrepresented biological samples, such as gene ontology terms, pathways, or protein domains, among the identified peptides.
- Comparative Analysis
To gain a deeper understanding of the peptide dataset, we offer comparative analysis services. This allows for the identification of differentially abundant peptides in multiple experimental conditions, providing insight into the dynamic changes occurring in peptide pools.
- Database Searching
We utilize various peptide identification algorithms, such as Mascot, SEQUEST, and X!Tandem, to match experimental mass spectra against comprehensive protein sequence databases.
Advantages of Peptideomics Functional Annotation and Enrichment Analysis
Our peptideomics functional annotation and enrichment analysis service offer several advantages:
- Expertise and experience: Creative Proteomics boasts a team of highly skilled scientists with extensive experience in peptidomic data analysis. Our experts stay up-to-date with the latest advancements in the field to provide cutting-edge services to our clients.
- Comprehensive analysis: We employ advanced bioinformatics tools and databases for thorough functional annotation and enrichment analysis.
- Customized solutions: We understand that each project is unique. Accordingly, we provide personalized consultation and tailor our analysis pipeline to specific research goals and requirements.
Our Analysis Techniques
Peptideomics functional annotation and enrichment analysis involves determining the functional properties and enrichment of identified peptides in a given sample.
- Database searching
- UniProtKB/Swiss-Prot: Centralized protein sequence database.
- NCBI Protein: Database containing protein sequences from various sources.
- Ensembl: Genome annotation project providing protein and gene sequences.
- RefSeq: Comprehensive archive of reference sequences.
- Sequence similarity and homology analysis
- BLAST (Basic Local Alignment Search Tool): Searches for similar peptide sequences in a sequence database.
- PSI-BLAST (Position-Specific Iterated BLAST): Enhanced version of BLAST for remote homology detection.
- HMMER (Hidden Markov Model based on biosequence analysis): Utilizes profiles of peptide families to identify homologous sequences.
- Functional annotation databases and tools
- Gene ontology (GO): Provides a hierarchical classification of gene function, cellular component, and biological processes.
- Kyoto encyclopedia of genes and genomes (KEGG)
- InterPro: Integrated resource for protein families, domains, and functional sites.
- Pfam: Database of protein families and domains.
- Pathway enrichment analysis
- Enrichr: Web-based tool for biological pathway enrichment analysis.
- DAVID (Database for Annotation, Visualization, and Integrated Discovery): Functional annotation and pathway analysis tool.
- Reactome: Provides curated knowledge on biological pathways and processes.
- GSEA (Gene Set Enrichment Analysis): Determines whether a priori defined sets of genes demonstrate statistically significant differences between phenotypes.
- Protein-protein interaction analysis
- STRING (Search Tool for the Retrieval of Interacting Genes/Proteins): Database and web resource for protein-protein interactions.
- Cytoscape: Visualization and analysis software for biological networks.
- BioGRID: Database of protein-protein and genetic interactions.
- Functional enrichment analysis
- GOEnrichmentAnalysis: R package for gene ontology enrichment analysis.
- clusterProfiler: R package for functional enrichment analysis and visualization.
- WebGestalt: Web-based tool for functional enrichment analysis using various databases.
Sample Requirements
- Experimental samples will not be returned, please back 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 samples with special requirements, please contact our staff for more information.
Our laboratory work begins in the R&D phase: different approaches and parameters are explored and tested on a small scale to identify successful approaches. Depending on customer requirements, successfully developed analysis programs can be further validated. Viability analysis will be performed on the client's samples after the analytical program has been successfully established. Please contact us today and unlock the potential of peptide analysis.
* For research use only. Not for use in diagnostic procedures!
Our customer service representatives are available 24 hours a day, 7 days a week.
