PXD023665

PXD023665 is an original dataset announced via ProteomeXchange.

Title	Feasibility of phosphoproteomics on left-over sample after RNA extraction (RNA-Bee)
Description	In daily practice biomolecules are usually extracted with their own specific protocols for downstream omics analysis. However, when sample material is limited, an all-in-one strategy is preferable. DNA, RNA and proteins can be isolated with phenol guanidine thiocyanate based extraction, yet lysis with Urea is the accepted standard for phosphoproteomic applications. Here we compared Urea with RNA-Bee mediated protein extraction for use in mass spectrometry (MS) based phosphoproteomics analysis of cells and tissues. We profile the DNA damage response after ionizing irradiation of U2OS cells as proof of principle for cultured human cells as well as mouse liver and three different human tissues. We show high overlap and similarity of phosphosite data and kinase activity for RNA-bee extraction when compared to standard Urea approach. Phenol guanidine thiocyanate lysis might thus be an appropriate way for multi-omics or MS profiling workflows in order to obtain several data types from a single sample.
HostingRepository	PRIDE
AnnounceDate	2021-04-22
AnnouncementXML	Submission_2021-04-21_23:22:49.278.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-19 04:41:37	ID requested
⏵ 1	2021-04-21 23:22:50	announced

Rolfs F, Piersma SR, Dias MP, Jonkers J, Jimenez CR, Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate. Mol Cell Proteomics, 20():100078(2021) [pubmed]

submitter keyword: RNAB, phenol guanidine thiocyanate, phosphoproteomics, tissue, cell line, lysis

Connie Ramona Jimenez
contact affiliation	Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	Amsterdam UMC
contact email	s.piersma@amsterdamumc.nl
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/2021/04/PXD023665

PRIDE project URI

• PRIDE
  1. PXD023665
     1. Label: PRIDE project
     2. Name: Feasibility of phosphoproteomics on left-over sample after RNA extraction (RNA-Bee)