CBI Mass Spectrometry

The Cancer Bioinformatics (CBI) Shared Resource offers mass spectrometry analysis services to help you gain biological insights from proteomic, metabolomic, and lipidomic data. We work with data generated by your lab, through the Proteomics and Metabolomics Cores, or from publicly available datasets. 

Our team provides practical guidance on experimental design and data analysis to ensure accurate and reproducible results, whether you are planning targeted panels or broader discovery studies.

Experimental Design & Capabilities

We assist with both global profiling and targeted analyses. This includes planning experiments to measure overall abundance differences, setting up targeted panels for lipid or protein profiling, and profiling post-translational modifications (e.g., phosphorylation) to track changes in cellular signaling. The data are produced using advanced mass spectrometry systems that support data-dependent and data-independent acquisition modes. We apply best practices in data analysis to ensure your data are processed accurately.

Data Processing & Analysis Pipelines

Our analysis pipelines are designed to produce accurate and reproducible results. The workflow typically includes:

Data Preprocessing

Filtering, aligning spectral data, and normalizing to account for variability between runs.

Identification and Quantification

Using established software tools to identify proteins, metabolites, or lipids and quantify changes across conditions.

Statistical Analysis

Applying statistical methods to identify significant changes.

Reporting

Generating detailed reports that include instrument performance, identification statistics, and quantitative results.

Pathway Enrichment

We can generate pathway enrichment reports that map significant changes in proteins, metabolites, or lipids onto curated metabolic and signaling pathways. These reports help identify the biological pathways affected by your experimental conditions.

For more information or to schedule a consultation, please contact the CBI Shared Resource.