CURTAIN – A unique web-based tool for exploration and sharing of MS-based proteomics data

Toan K. Phung (Lead / Corresponding author), Kerryn Berndsen, Rosamund Shastry, Tran L. C. H. B. Phan, Miratul M. K. Muqit, Dario R. Alessi (Lead / Corresponding author), Raja S. Nirujogi (Lead / Corresponding author)

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Abstract

To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data, we created online tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info) with an accompanying series of video tutorials (https://www.youtube.com/@CURTAIN-me6hl). These are designed to enable non-MS experts to interactively peruse 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 allow assessment of overall experimental quality by correlation matrix and profile plot analysis. After making a selection of protein "hits", the user can analyze 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. CURTAIN-PTM also links with the Kinase Library to predict upstream kinases that may 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 also reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open source, enabling researchers to share and maximize the impact of their proteomics data. We advocate that MS data published in volcano plot format be reported containing a shareable CURTAIN weblink, thereby allowing readers to better analyze and exploit the data.

Original languageEnglish
Article numbere2312376121
Number of pages12
JournalProceedings of the National Academy of Sciences
Volume121
Issue number7
Early online date7 Feb 2024
DOIs
Publication statusPublished - 13 Feb 2024

Keywords

  • PTM
  • bioinformatics
  • mass spectrometry
  • proteomics
  • sharing data

ASJC Scopus subject areas

  • General

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