PXD056598

PXD056598 is an original dataset announced via ProteomeXchange.

Title	A multi-laboratory assessment of label-free quantification performance for high dynamic range samples across different instrument platforms
Description	Human plasma mirrors an individual´s health state and is routinely collected during clinical care for diagnostic purposes. As a potentially rich source of biomarkers, plasma continues to be a primary focus of biomedical and clinical pursuits until today. Due to its unbiased nature, liquid chromatography-mass spectrometry (LC-MS)-based proteomics has become a key method for the discovery of novel plasma biomarkers. However, MS-based approaches are challenged by the high dynamic range of plasma proteins. In the present study, we generated a multispecies sample set based on a human tryptic plasma digest which contains varying spike-in levels of tryptically digested yeast and E. coli (PYE) proteomes addressing the challenges of a high protein dynamic range. With the aim to benchmark and evaluate the quantitative performance of neat plasma analysis, the sample set was distributed and analysed on various state-of-the-art LC-MS platforms across twelve different sites. The resulting data set encompasses in total 1,116 individual LC-MS runs and was centrally analyzed. Data sets derived from different setups were compared in terms of identifications, data completeness, accuracy, precision, as well as reproducibility. The acquisition mode was one of the main factors impacting proteome coverage, reproducibility and data completeness. Beside the acquisition mode, other parameters, such as gradient length, cycle time, instrument settings etc. affected proteomic depth as well as accuracy and precision of the quantitative measurements. The present dataset poses a valuable resource for further optimizing LC-MS workflows with the aim to enhance the accuracy and reproducibility of plasma proteome analysis, crucial for clinical biomarker discovery and verification.
HostingRepository	jPOST
AnnounceDate	2025-08-29
AnnouncementXML	Submission_2025-08-29_04:53:38.868.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Malte Sielaff
SpeciesList	scientific name: cellular organisms; NCBI TaxID: 131567; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480; Orbitrap Fusion Lumos; Q Exactive HF; Q Exactive HF-X; ZenoTOF 7600; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-08 01:25:30	ID requested
⏵ 1	2025-08-29 04:53:39	announced

Dataset with its publication pending

submitter keyword: LFQ, plasma proteomics, PYE, multispecies proteome standard

Ute Distler
lab head
Malte Sielaff
contact affiliation	University Medical Center of the Johannes Gutenberg-University Mainz
dataset submitter

jPOST dataset URI

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