Development of CURTAIN and CURTAIN-PTM unique web-based tools for exploration and sharing of MS-based proteomics and PTM data

Toan Phung with Raja Nirujogi
Toan Phung with Raja Nirujogi

To facilitate the analysis of mass spectrometry-based proteomics data, MRCPPU researchers Toan Phung working closely with Raja Nirujogi have generated free-to-use interactive tools termed CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info).

The paper describing the CURTAIN and CURTAIN-PTM tools has just been published (https://www.pnas.org/doi/10.1073/pnas.2312676121)

CURTAIN-PTM and CURTAIN are designed to enable non-MS experts to interactively peruse and analyse volcano plots and deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots and exported in publication-ready format.

They also allows users to assess overall experimental quality of the mass spectrometry data by performing correlation matrix and profile plot analysis.

After selecting protein "hits", the user can analyse known domain structure, AlphaFold predicted structure, reported interactors, relative expression as well as disease links.

CURTAIN-PTM permits analysis of all identified PTM sites on protein(s) of interest with selected databases. It also links with the Kinase Library to predict upstream kinases that may phosphorylate sites of interest.

CURTAIN and CURTAIN-PTM are designed to be easy-to-use tools. This was illustrated in the paper by analysis of experimental proteomics and phosphoproteomics data generated by Kerryn Berndsden and Tran Phan in the Alessi laboratory.

We advocate that all MS volcano plot data be published containing a shareable CURTAIN weblink, thereby allowing readers to better analyses and exploit the data. This would enable researchers to maximise impact of their data.

Curatin a unique web based tool for exploration and sharing of MS-based proteomics data

To help users familiarize themselves with the tool, Rosamund Shastry a postdoc in the Muqit laboratory, created a series of video tutorials available on a dedicated YouTube channel (https://www.youtube.com/@CURTAIN-me6hl).

We are enormously grateful to the support of Aligning Science Across Parkinson's: ASAP (https://parkinsonsroadmap.org) for inspiring and enabling this project.