Lightning Talk & Poster 28th Annual Lorne Proteomics Symposium 2023

C3, a collection of data management, visualization and exploration web applications for proteomics data analysis (#34)

Toan K Phung 1 2 , Kerryn Berndsen 1 2 , Tran Phan 1 2 , Raja S Nirujogi 1 2 , Dario R Alessi 1 2
  1. MRC PPU, University of Dundee, Dundee, Dundee City, United Kingdom
  2. Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Michael J. Fox Foundation, Chevy Chase, MD, United States

Visualization of differential expression mass spectrometry data is normally undertaken by a mass spectrometry expert using software suites such as Perseus or R that require computer installation and significant expertise to use. This makes it difficult for researchers without such software or expertise to obtain the visualizations they want on their own. Additionally, it makes it difficult for the person with the skills, software and expertise to share the data with non-expert collaborators. To circumnavigate this, we created a collection of free to use, open-source, and web-based tools that can perform data management, data visualization, and data exploration of mass spectrometry-based proteomics data called “C3”. C3 comprises of “Celsus”, “Curtain” (http://curtain.proteo.info) and “CurtainPTM” (http://curtainptm.proteo.info).

Across the 3 applications, these tools share various common data visualizations such as volcano, profile, bar and network charts. Celsus puts the focus on being a single repository for storing all of your analytical output from multiple projects where you can also quickly search for any proteins of interest across stored results. Being a web-based application, only one instance is needed for your whole laboratory’s data to be accessed within an internal network or across the internet.

Curtain and CurtainPTM, however, have a different focus toward sharing a particular experiment’s results along with visual customization for certain hits or proteins of interest. Here, the application also aggregates additional information such as summary of known biological function, domain structure, AlphaFold structure and characterized interactors of each selected protein. The users can search for an individual protein or a collection of proteins by providing the gene names, UniProt accession ids, or using our list of built-in protein collections associated with various themes such as Parkinson’s Disease, Alzheimer’s Disease, kinases, phosphatases, mitochondrial proteins, glycosylation proteins. In CurtainPTM (PTM specific version), it also allows phospho-proteomic and other post-translational proteomic data to be easily analysed and visualised in a similar manner. Identified phosphorylation sites and how these vary between experimental samples can be plotted and compared with phosphorylation site data reported within the PhosphoSitePlus database. The data, as well as the proteins or PTMs that the user chose to highlight, can be sent onto anyone along with any user-determined visualization customization through a unique web link that can be saved and shared.