CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data

ABSTRACT: To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data we created two tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info). They are designed to enable the non-MS expert to interactively pursue volcano plots, deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots allowing statistical analysis and export of plots in SVG format. They also permit assessment of experimental quality by correlation matrix and profile plot. Within CURTAIN, the user can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression and UniProt disease, pharmaceutical and mutagenesis information on all selected hits. CURTAIN-PTM permits comparison of all identified PTM sites on protein(s) of interest with selected databases. For phosphorylation site analysis CURTAIN-PTM links with the Kinase Library to predict upstream kinases that phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson’s LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We re-analyzed a ubiquitinylation dataset, characterizing PINK1-Parkin pathway in primary neurons, revealing new data of interest not previously highlighted. CURTAIN and CURTAIN-PTM are free to use and open-source and will enable researchers to share their data and maximize the impact of proteomics data. We advocate that published proteomic data be submitted containing a shareable CURTAIN web-link, allowing readers to better explore the data.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Epithelial Cell

DISEASE(S): Parkinson's Disease

SUBMITTER: Raja Sekhar Nirujogi  

LAB HEAD: Dario R. Alessi

PROVIDER: PXD043806 | Pride | 2023-12-21

REPOSITORIES: Pride