Bioinformatics
The Proteomics and Metabolomics Core provides high-throughput bioinformatics services and data analysis solutions to enable translation of data into knowledge. The bioinformatics team leverages the Cedars-Sinai state-of-the-art infrastructure as well as domain experts in the fields of proteomics, bioinformatics, data science and programming to help address research questions.
Two main service areas include:
- Basic bioinformatics support for label-free, data-dependent and data- independent acquisition-mass spectrometry
- Extended bioinformatics support for advanced data analytics, data visualization, pathway analysis and new tool/pipeline development
Tools Developed and Managed by Bioinformatics Team
Users of the facility have convenient access to an easy-to-use, interactive, web-based platform for proteomics data analysis. Our platform has a powerful, advanced, high-performance cluster, computing-based distributed architecture comprising of 4 key components—data connectors, cognitive core, workflow automation, and visualization and reporting—that help us address ’omics challenges end-to-end. The platform is highly customizable for integration of custom algorithms and domain wrappers based on research needs, and most of the functionalities are available as a secured web application—making it a customizable and scalable solution for all bioinformatics needs.
For more information, please contact us.
Protein citrullination (or deimination) is an irreversible post-translational modification (PTMs) implicated in several physiological and pathological processes that is difficult to identify and validate accurately. CitFinder is a tool that aims to overcome this limitation by analyzing mass spectrometry-based spectral libraries to confidently identify and validate citrullinated sites.
For more information, please visit github.com/csmc-vaneykjlab/CitFinder.
Protein Interaction Network Extractor (PINE) is a fully automated, user-friendly, graphical user interface-based tool suitable for the study of global proteome and PTMs with robust visualization of their interaction or enriched functional networks. PINE also supports overlaying differential expression, statistical significance thresholds and PTM sites on functionally enriched visualization networks to gain insights into proteome-wide regulatory mechanisms, as well as how PTMs might regulate protein-protein interactions.
For more information, please visit github.com/csmc-vaneykjlab/pine.
The plasma component of blood has long been used as the most important biofluid for diagnostic and prognostic clinical analyses. PlasmaPilot was developed based on experimentally defined, bottom-up human plasma proteomics data with the goal of providing a prospective guide for assay development.
For more information, please visit plasmapilot.herokuapp.com.
Bioinformatics also provide extended bioinformatics support for mass spectrometry tools (e.g., Skyline, Scaffold), pathway/network analysis tools (e.g., IPA, Cytoscape, KEGG, Reactome, David, STRING) and data analytics/visualization tools (e.g., PCA, Volcano Plot, Heatmap, Venn, Clustering, Blast, GO Enrichment, Sequence Logos, Kinase prediction, etc.) as well as support for publication/grants.
For more information, please contact us.
Our team’s diverse bioinformatics expertise and access to data from rich and diverse cohorts empower new tool/pipeline development. The bioinformatics team is continuously involved in new tool/pipeline development projects.
To find out more or to become part of our next development project, please contact us today.
Examples of Bioinformatics Analyses We Can Perform
Bioinformatics Consultation Request
Schedule a consultation to discuss the full potential of bioinformatics approaches to address your research needs.
Have Questions or Need Help?
Contact us if you have questions or would like to learn more about the Proteomics & Metabolomics Core at Cedars-Sinai.