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Cited by 18Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic NetworksMass Spectrometry Techniques and Applications

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

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Phung, Toan K., Berndsen, Kerryn, Shastry, Rosamund, Phan, Tran L. C. H. B., Muqit, Miratul M. K., Alessi, Dario R., Nirujogi, Raja S.·2024·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2312676121PMC PMC10873628

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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.

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Metadata

Authors
Phung, T. K., Berndsen, K., Shastry, R., Phan, T. L. C. H. B., Muqit, M. M. K., Alessi, D. R., & Nirujogi, R. S.
Affiliations
University of Dundee (GB)
Corresponding author
  • Phung, Toan K.
  • Alessi, Dario R.
  • Nirujogi, Raja S.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2024-02-07
Volume
121
Issue
7
Pages
e2312676121-e2312676121
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.2312676121
PMC
PMC10873628
OpenAlex
W4391594220
Cited by
18
References
3
Citations by year
2026: 5 · 2025: 6 · 2024: 6
FWCI
2.11
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
  • Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
Funders
  • Aligning Science Across Parkinson's (000463)
  • UKRI | Medical Research Council (MC_UU_00018/1)
  • Wellcome Trust (210753/Z/18/Z)
  • Novo Nordisk (N/A)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
curtains, web-based data exploration, volcano plot, phosphorylation sites, post-translational modification, LRRK2, Parkinson's disease, PINK1/Parkin pathway, ubiquitination, primary neurons, AlphaFold protein structure, interactors
MeSH terms
Phosphorylation, Protein Processing, Post-Translational, Proteins, Software, Mass Spectrometry, Internet, Proteomics

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