PXD043806 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data |
Description | 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. |
HostingRepository | PRIDE |
AnnounceDate | 2023-12-21 |
AnnouncementXML | Submission_2023-12-21_11:20:27.156.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Raja Sekhar Nirujogi |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-07-15 00:50:43 | ID requested | |
⏵ 1 | 2023-12-21 11:20:28 | announced | |
Publication List
10.1126/sciadv.abj0722; |
10.1042/bcj20190608; |
Antico O, Ordureau A, Stevens M, Singh F, Nirujogi RS, Gierlinski M, Barini E, Rickwood ML, Prescott A, Toth R, Ganley IG, Harper JW, Muqit MMK, Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1. Sci Adv, 7(46):eabj0722(2021) [pubmed] |
Malik N, Nirujogi RS, Peltier J, Macartney T, Wightman M, Prescott AR, Gourlay R, Trost M, Alessi DR, Karapetsas A, Phosphoproteomics reveals that the hVPS34 regulated SGK3 kinase specifically phosphorylates endosomal proteins including Syntaxin-7, Syntaxin-12, RFIP4 and WDR44. Biochem J, 476(20):3081-3107(2019) [pubmed] |
Keyword List
submitter keyword: Bioinformatics, PTM, BromoTAG,Proteomics |
Contact List
Dario R. Alessi |
contact affiliation | Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K. |
contact email | d.r.alessi@dundee.ac.uk |
lab head | |
Raja Sekhar Nirujogi |
contact affiliation | MRC Protein Phosphorylation Unit, university of Dundee |
contact email | rnirujogi@dundee.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD043806 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD043806
- Label: PRIDE project
- Name: CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data