PXD020261

PXD020261 is an original dataset announced via ProteomeXchange.

Title	Multi-platforms approach for plasma: complementarity of Olink PEA technology to DIA-based mass spectrometry-based protein profiling
Description	Plasma proteome is the ultimate target for the biomarker discovery. It stores an endless amount of information on the pathophysiological status of a living organism, which however is still difficult to comprehensively access. The high structural complexity of the plasma proteome can be addressed by using a system-wide and unbiased tool such as mass spectrometry (LC-MS/MS) or highly sensitive targeted immunoassays as Olink Proximity Extension Assays. We have tested the performance of LC-MS/MS in data –dependent and -independent acquisition modes and Olink PEA to measure circulating plasma proteins in 173 human plasma samples from a southern Germany population-cohort. More than 300 proteins were measured by both LC-MS/MS approaches, mainly including high abundance functional plasma proteins. By using the Olink PEA technology we measured 728 plasma proteins, covering a broad dynamic range with high sensitivity down to pg/ml levels. We found 35 overlapping proteins in all three analytical platforms, predominantly secreted and highly abundant in plasma. The complementarity of the platforms was assessed by veryfing the reproducibility of data distributions, statistical correlation of measurements and gender-based differential expression analysis. Our work highlights the limitations and the advantages of both targeted and untargeted approaches and prove their complementarity. We demostrated that by combining the results of the three platforms we gain in depth proteome coverage as well as biological insights.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:35:22.753.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christine von Toerne
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-08 06:36:15	ID requested
1	2022-03-10 02:42:35	announced
⏵ 2	2024-10-22 05:35:23	announced	2024-10-22: Updated project metadata.

Petrera A, von Toerne C, Behler J, Huth C, Thorand B, Hilgendorff A, Hauck SM, Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling. J Proteome Res, 20(1):751-762(2021) [pubmed]

10.1021/acs.jproteome.0c00641;

submitter keyword: Olink technology, DIA-MS,KORA: Cooperative Health Research in the Region of Augsburg

Stefanie Melanie Hauck
contact affiliation	Research Unit Protein Science, Helmholtz Zentrum München, Germany
contact email	hauck@helmhotz-muenchen.de
lab head
Christine von Toerne
contact affiliation	Helmholtz Zentrum München
contact email	vontoerne@helmholtz-muenchen.de
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/2022/03/PXD020261

PRIDE project URI

• PRIDE
  1. PXD020261
     1. Label: PRIDE project
     2. Name: Multi-platforms approach for plasma: complementarity of Olink PEA technology to DIA-based mass spectrometry-based protein profiling