Quantitative Proteomics

Next-generation sequencing in the post-genomic world has undergone near-continuous advances in power and cost-effectiveness, making it an increasingly common tool in the researcher’s toolbox. However, changes in cellular signaling and other molecular interactions often taken place at the protein level and cannot be detected by genomic or transcriptomic studies.

The ability to quantitatively measure untargeted changes in protein, peptide, and post-translation modification (PTM) levels is an underappreciated approach to understand cellular and organismal response to genetic or environmental perturbation. Modern mass spectrometry makes possible the detection and quantitative measurement of tens of thousands of individual proteins simultaneously, enabling a wide range of experimental approaches to detect differential abundance of proteins and PTMs as well as protein conformational change. Interpretation of the resulting data requires an understanding of the unique challenges and potential pitfalls unique to mass spectrometry-based proteomics.

BASE₂BIO can help.

Members of our team have considerable experience designing and analyzing modern quantitative proteomics experiments. They have authored software for quantitative analysis of isobarically labeled samples and modeling of proteome-wide thermal stability based on mass spectrometry. We can help with experimental design to ensure sufficient data depth and statistical power to answer your specific research questions. Our scalable cloud-based data analysis pipelines, either pre-built or customized to your needs, utilize cutting-edge mass spectrometry software and best practices of reproducible research to make sure your methods and results meet the requirements of top proteomics and other science journals.

Please see our publications page for examples of past proteomics research by our team members. If you would like to know more about how we can help with your quantitative proteomics data analysis, please fill out the contact form below.