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

• 成果类型: Article
• 署名作者: Phung, Toan K.; Berndsen, Kerryn; Shastry, Rosamund; Phan, Tran L. C. H. B.; Muqit, Miratul M. K.; Alessi, Dario R.; Nirujogi, Raja S.
• 署名单位: University of Dundee
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-12399
• DOI: 10.1073/pnas.2312676121
• 发表日期: 2024-02-07
• 关键词: mass-spectrometry; peptide identification; comprehensive analysis; data-resource; platform; reveals; package

摘要

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. Significance To facilitate the analysis of mass spectrometry - based proteomics data, we have generated free - to - use interactive tools termed CURTAIN and CURTAINPTM. These enable users to save analyzed proteomics data as an interactive and customizable volcano plot which can be shared with a weblink that can be included in publications. This permits other researchers to visualize and further analyze data contained within the volcano plots. CURTAIN and CURTAINPTM serve as a repository for mass spectrometry-based proteomics data as well as an easy - to - use interactive analysis and visualization tool, allowing researchers to maximize the impact of their data. To help users familiarize themselves with the tool, we have created a series of video tutorials available on a dedicated YouTube channel (https://www.youtube.com/@ CURTAINme6hl).