PXD069060

PXD069060 is an original dataset announced via ProteomeXchange.

Title	Plasma Proteomics Benchmarking and Optimisation/ Plasma proteomics across three generations of mass spectrometry instruments: lessons for optimising biomarker discovery
Description	In biomarker discovery phases clinical proteomics provides large-scale identification and quantification of proteins in donor samples. For these studies plasma is the most frequently used biofluid, as it reflects both physiological and pathological states of the circulating proteome. However, the vast dynamic range of proteins in plasma remains a significant challenge, where low-abundance biomarkers are suppressed by high-abundance proteins, despite substantial technological improvements. Often the focus of improving outcomes in plasma proteomic workflows are within the biofluid’s sample preparation, although adjusting MS methods dramatically improves detection and sampling of lower abundance proteins. Herein we have benchmarked various liquid chromatography (LC) and data-independent acquisition (DIA) methods across three generations of mass spectrometry instruments: timsTOF Pro (2017), Orbitrap Eclipse (2020), and Orbitrap Astral (2023). This study explored 27 methods across 200 hours of instrument acquisition time, encompassing varying LC, MS, and database searching workflows. While each instrument generation significantly improved performance, each instrument also revealed a unique and different tuneable range to improve performance in plasma samples, highlighting the benefit of investing in plasma-specific method development for any mass spectrometer. We also evaluated the detection and quantification capabilities of each instrument via a unique approach of mixing paired Platelet Poor Plasma (PPP) and Platelet Rich Plasma (PRP), introducing linear contamination markers for quantitative assessment. This approach tested each instrument's sensitivity to detect low-abundance peptides and evaluated their quantitative accuracy. Lastly, we performed testing of the Orbitrap Astral’s parallel ion processing capabilities with the aim of improving low-abundance protein identifications using gas-phase enrichment (GPE). More specifically, we show that optimisation of MS2 AGC targets and injection time enhanced GPE of low-abundance peptides, improving detection in plasma samples.
HostingRepository	PRIDE
AnnounceDate	2026-04-22
AnnouncementXML	Submission_2026-04-21_19:55:57.050.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jack Edwards
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse; timsTOF Pro; Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-01 17:15:15	ID requested
⏵ 1	2026-04-21 19:55:58	announced

10.1002/pmic.70127;

Edwards J, Multari DH, Dite T, Binos S, Shugg C, Webb AI, Dagley LF, Emery-Corbin SJ, Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method Optimisation. Proteomics, ():e70127(2026) [pubmed]

submitter keyword: plasma proteomics, Astral, clinical proteomics, LCMS

Laura Dagley
contact affiliation	Lab Head: WEHI
contact email	dagley.l@wehi.edu.au
lab head
Jack Edwards
contact affiliation	WEHI, CSL Seqirus
contact email	jack.edw02@gmail.com
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/2026/04/PXD069060

PRIDE project URI

• PRIDE
  1. PXD069060
     1. Label: PRIDE project
     2. Name: Plasma Proteomics Benchmarking and Optimisation/ Plasma proteomics across three generations of mass spectrometry instruments: lessons for optimising biomarker discovery