proteinBASE - An online visualization platform for proteomics datasets

Welcome to proteinBASE

This tool allow users to interactively explore mass-spectrometry proteomic datasets. Using a rich suite of dynamic visualisation tools, proteinBASE transforms complex datasets into accessible insights to empower users to investigate protein expression patterns and biological signatures across label-free quantitative proteomics studies. For all outputs from the application, please acknowledge proteinBASE and the Manchester Cell-Matrix Centre.

Visualization tools available in proteinBASE

Principal Component Analysis (PCA)

PCA plots help identify major sources of variability across samples and replicates. They allow users to explore each dataset individually and visualise patterns linked to key biological or experimental factors, such as treatment groups, conditions, or disease states.

Hierarchical Clustering Heatmap

Heatmaps provide an overview of protein expression relationships across samples, enabling the detection of trends, co-expression patterns, and sample clustering. These visualisations help assess replicate consistency and highlight biologically meaningful structures within the dataset.

Explore individual proteins using interactive bar and box plots. These plots display quantile-normalised, log2-transformed abundance values, making it easy to compare protein levels across treatments, disease conditions, or experimental groups and to highlight biologically relevant differences.

Useful Links

  1. University of Manchester https://www.manchester.ac.uk/
  2. Manchester Cell-Matrix Centre https://www.manchester.ac.uk/
  3. Lennon Lab https://lennonlab.wixsite.com/home

Proteomics repositories

  1. ProteomeXchange https://www.proteomexchange.org/
  2. PRIDE: Proteomics Identification Database https://www.ebi.ac.uk/pride/
  3. MassIVE https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp?redirect=auth

Cell-Matrix Resources

  1. Basement MembraneBASE: A resource for basement membrane research https://bmbasedb.manchester.ac.uk/
  2. The Matrisome Project https://naba.lab.uic.edu/the-matrisome-project
  3. MatrixDB - The extracellular matrix interaction database https://matrixdb.univ-lyon1.fr/

Contact us

Please get in touch if you have any questions about proteinBASE. Send us an email: proteinbase@manchester.ac.uk

Our team