PXD023148

PXD023148 is an original dataset announced via ProteomeXchange.

Title	iEvaluation of spin columns for human plasma depletion to facilitate MS-based proteomics analysis of SARS-cov-2 positive plasman columns for human plasma depletion to facilitate MS-based proteomics analysis of SARS-cov-2 positive plasma
Description	the benefit on the number of identified proteins is well documented and the depletion step remains widely used in in-depth proteomics. Recently, single-use depletion spin columns have been developed (i.e High Select™ Top14 Abundant Protein Depletion Mini Spin Columns, Thermo) which greatly reduces the handling time compared to HPLC columns and enables parallel depletion of multiple samples which has not been possible in the previous multiple use columns. The covid-19 pandemic also shed light on the need of a depletion protocol easily adapted in a BSL3 facility without needs for special equipment such as an HPLC system, as heat inactivation of the virus prior to depletion could affect the depletion efficacy. The aim of this study was to evaluate the use of single-use spin columns for high abundant protein depletion prior to in-depth MS based global plasma analysis, to improve throughput while maintaining high proteome coverage and high reproducibility.
HostingRepository	PRIDE
AnnounceDate	2021-07-30
AnnouncementXML	Submission_2021-07-29_23:38:59.774.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Georgios Mermelekas
SpeciesList	scientific name: Macaca mulatta (Rhesus macaque); NCBI TaxID: 9544; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-15 08:14:01	ID requested
⏵ 1	2021-07-29 23:39:00	announced

Cao X, Sandberg A, Ara, ú, jo JE, Cvetkovski F, Berglund E, Eriksson LE, Pernemalm M, Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma. J Proteome Res, 20(9):4610-4620(2021) [pubmed]

submitter keyword: human, plasma, depletion, spin-column, SARS-cov-2, mass spectrometry, proteomics

Maria Pernemalm
contact affiliation	Dept. Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
contact email	maria.pernemalm@ki.se
lab head
Georgios Mermelekas
contact affiliation	Karolinska Institutet
contact email	georgios.mermelekas@scilifelab.se
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/PXD023148

PRIDE project URI

• PRIDE
  1. PXD023148
     1. Label: PRIDE project
     2. Name: iEvaluation of spin columns for human plasma depletion to facilitate MS-based proteomics analysis of SARS-cov-2 positive plasman columns for human plasma depletion to facilitate MS-based proteomics analysis of SARS-cov-2 positive plasma