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PreprintCited 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, Phan, Tran Le Cong Huyen Bao, Muqit, Miratul M. K., Alessi, Dario R., Nirujogi, Raja S.·2023·Proceedings of the National Academy of Sciences
DOI 10.1101/2023.07.25.550405PMC PMC10873628

Preprint — published as 10.1073/pnas.2312676121 · Paper page

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Abstract

To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data we created tools called CURTAIN ( https://curtain.proteo.info ) and CURTAIN-PTM ( https://curtainptm.proteo.info ). These enable the non-MS expert to interactively peruse volcano plots; deconvolute primary experimental data to individual replicates that 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, disease and pharmaceutical links, and mutagenesis information on all selected hits. Moreover, CURTAIN-PTM permits the comparison of all identified PTM sites on protein(s) of interest with PTM information contained within 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 reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing new data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open-source and will enable researchers to share and maximize the analysis and impact of their proteomics data. We advocate that differential expression proteomic data should be published containing a shareable CURTAIN web-link, allowing readers to better explore their data. Significance Statement: To enable non-experts to better share and explore mass spectrometry data, we have generated using open-source software, interactive tools termed CURTAIN and CURTAIN-PTM. These tools enable users’ to save their analysis sessions with a sharable unique web-link, enabling other researchers to visualize and further analyze these datasets. These links can also be reported in publications allowing readers to further survey the reported data. We discuss benefits for the research community of publishing proteomic data containing a shareable web-link.

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Metadata

Authors
Phung, T. K., Berndsen, K., 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
openRxiv
Published
2023-07-25
Volume
121
Issue
7
Pages
e2312676121-e2312676121
ISSN
0027-8424 (ISSN-L)
DOI
10.1101/2023.07.25.550405
PMC
PMC10873628
OpenAlex
W4391594220
Cited by
18
References
1
Citations by year
2026: 5 · 2025: 6 · 2024: 6 · 2023: 1
FWCI
2.11
Type
journal article
Language
en
Open access
Licence
cc-by
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
  • Michael J. Fox Foundation for Parkinson's Research (ASAP‐000463)
  • GlaxoSmithKline
  • Merck KGaA
  • Wellcome Trust (210753/Z/18/Z)
  • UK Research and Innovation (MC_UU_00018/1)
  • Aligning Science Across Parkinson’s (000463)
  • Novo Nordisk
  • Novo Nordisk Foundation Center for Basic Metabolic Research
  • Medical Research Council (MC_UU_00018/1)
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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