PXD011971

PXD011971 is an original dataset announced via ProteomeXchange.

Title	Comparison of proteomic and phospho-proteomic analysis upon urea extraction and triple extraction
Description	The goal of the present project was to investigate the applicability of a triple extraction (”TE”), which yields RNA, DNA and protein in a single procedure, for gel-free mass spectrometry-based proteomics. Proven successful for large-scale transcriptomics and genomics, we examined TE compatibility with mass spectrometry-based proteomics and phospho-proteomics by comparison to a urea standard processing. For whole proteome, peptides were fractionated using SAX; for phosphorylation analysis, modifications were enriched using TiO2 columns. We here demonstrate the efficiency of TE protocol for shotgun proteomics, providing similar results as urea-derived samples both at the qualitative and quantitative levels. The study of phosphorylation events is likewise compatible with TE, which actually results in a higher number of correctly localized sites than urea, while the nature of extracted sites appears somewhat distinct between both techniques. We thus conclude that our protocol is well suited for proteomics and as efficient as other more widely used workflows for mass spectrometry-based analysis.
HostingRepository	PRIDE
AnnounceDate	2021-07-20
AnnouncementXML	Submission_2021-07-19_21:58:00.448.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guillaume Arras
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-07 01:07:39	ID requested
⏵ 1	2021-07-19 21:58:01	announced

Sanchez-Quiles V, Shi MJ, Dingli F, Krucker C, Loew D, Bernard-Pierrot I, Radvanyi F, Triple extraction method enables high quality mass spectrometry-based proteomics and phospho-proteomics for eventual multi-omics integration studies. Proteomics, 21(16):e2000303(2021) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: SAX, TiO2, urea, triple extraction, bladder cancer

Damarys Loew
contact affiliation	Laboratoire de Spectrometrie de Masse Proteomique Institut Curie PSL Research University
contact email	Damarys.Loew@curie.fr
lab head
Guillaume Arras
contact affiliation	Institut Curie
contact email	guillaume.arras@curie.fr
dataset submitter

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/2021/07/PXD011971

PRIDE project URI

• PRIDE
  1. PXD011971
     1. Label: PRIDE project
     2. Name: Comparison of proteomic and phospho-proteomic analysis upon urea extraction and triple extraction