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000281523 1001_ $$00000-0002-8031-6384$$aDistler, Ute$$b0
000281523 245__ $$aMulticenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set.
000281523 260__ $$a[London]$$bSpringer Nature$$c2025
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000281523 520__ $$aHuman plasma is routinely collected during clinical care and constitutes a rich source of biomarkers for diagnostics and patient stratification. Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a key method for plasma biomarker discovery, but the high dynamic range of plasma proteins poses significant challenges for MS analysis and data processing. To benchmark the quantitative performance of neat plasma analysis, we introduce a multispecies sample set based on a human tryptic plasma digest containing varying low level spike-ins of yeast and E. coli tryptic proteome digests, termed PYE. By analysing the sample set on state-of-the-art LC-MS platforms across twelve different sites in data-dependent (DDA) and data-independent acquisition (DIA) modes, we provide a data resource comprising a total of 1116 individual LC-MS runs. Centralized data analysis shows that DIA methods outperform DDA-based approaches regarding identifications, data completeness, accuracy, and precision. DIA achieves excellent technical reproducibility, as demonstrated by coefficients of variation (CVs) between 3.3% and 9.8% at protein level. Comparative analysis of different setups clearly shows a high overlap in identified proteins and proves that accurate and precise quantitative measurements are feasible across multiple sites, even in a complex matrix such as plasma, using state-of-the-art instrumentation. The collected dataset, including the PYE sample set and strategy presented, serves as a valuable resource for optimizing the accuracy and reproducibility of LC-MS and bioinformatic workflows for clinical plasma proteome analysis.
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000281523 650_7 $$2NLM Chemicals$$aBlood Proteins
000281523 650_7 $$2NLM Chemicals$$aProteome
000281523 650_7 $$2NLM Chemicals$$aBiomarkers
000281523 650_2 $$2MeSH$$aHumans
000281523 650_2 $$2MeSH$$aProteomics: methods
000281523 650_2 $$2MeSH$$aChromatography, Liquid: methods
000281523 650_2 $$2MeSH$$aBlood Proteins: analysis
000281523 650_2 $$2MeSH$$aBlood Proteins: metabolism
000281523 650_2 $$2MeSH$$aProteome: analysis
000281523 650_2 $$2MeSH$$aBenchmarking
000281523 650_2 $$2MeSH$$aReproducibility of Results
000281523 650_2 $$2MeSH$$aMass Spectrometry: methods
000281523 650_2 $$2MeSH$$aBiomarkers: blood
000281523 650_2 $$2MeSH$$aEscherichia coli: metabolism
000281523 650_2 $$2MeSH$$aPlasma: chemistry
000281523 7001_ $$aYoo, Han Byul$$b1
000281523 7001_ $$aKardell, Oliver$$b2
000281523 7001_ $$aHein, Dana$$b3
000281523 7001_ $$aSielaff, Malte$$b4
000281523 7001_ $$aScherer, Marian$$b5
000281523 7001_ $$aJozefowicz, Anna M$$b6
000281523 7001_ $$aLeps, Christian$$b7
000281523 7001_ $$00000-0002-9467-1213$$aGomez-Zepeda, David$$b8
000281523 7001_ $$00000-0002-4132-4322$$avon Toerne, Christine$$b9
000281523 7001_ $$00000-0002-3422-4083$$aMerl-Pham, Juliane$$b10
000281523 7001_ $$aBarth, Teresa K$$b11
000281523 7001_ $$0P:(DE-2719)2812852$$aTüshaus, Johanna$$b12
000281523 7001_ $$0P:(DE-2719)9001718$$aGiesbertz, Pieter$$b13
000281523 7001_ $$aMüller, Torsten$$b14
000281523 7001_ $$aKliewer, Georg$$b15
000281523 7001_ $$aAljakouch, Karim$$b16
000281523 7001_ $$aHelm, Barbara$$b17
000281523 7001_ $$00009-0001-1798-4347$$aUnger, Henry$$b18
000281523 7001_ $$00000-0001-9572-9686$$aFrey, Dario L$$b19
000281523 7001_ $$00000-0001-9321-2069$$aHelm, Dominic$$b20
000281523 7001_ $$00000-0002-7151-9913$$aSchwarzmüller, Luisa$$b21
000281523 7001_ $$aPopp, Oliver$$b22
000281523 7001_ $$aQin, Di$$b23
000281523 7001_ $$00009-0001-6333-5233$$aWudy, Susanne I$$b24
000281523 7001_ $$00000-0003-4692-0681$$aSinn, Ludwig Roman$$b25
000281523 7001_ $$00000-0002-4332-1280$$aMergner, Julia$$b26
000281523 7001_ $$00000-0002-6131-7322$$aLudwig, Christina$$b27
000281523 7001_ $$00000-0003-2993-8249$$aImhof, Axel$$b28
000281523 7001_ $$00000-0002-9094-1677$$aKuster, Bernhard$$b29
000281523 7001_ $$0P:(DE-2719)2181459$$aLichtenthaler, Stefan F$$b30
000281523 7001_ $$aKrijgsveld, Jeroen$$b31
000281523 7001_ $$aKlingmüller, Ursula$$b32
000281523 7001_ $$00000-0002-2245-528X$$aMertins, Philipp$$b33
000281523 7001_ $$00000-0002-2244-5081$$aCoscia, Fabian$$b34
000281523 7001_ $$00000-0001-9535-7413$$aRalser, Markus$$b35
000281523 7001_ $$00000-0001-9792-3861$$aMülleder, Michael$$b36
000281523 7001_ $$00000-0002-1630-6827$$aHauck, Stefanie M$$b37
000281523 7001_ $$00000-0003-3034-0017$$aTenzer, Stefan$$b38
000281523 773__ $$0PERI:(DE-600)2553671-0$$a10.1038/s41467-025-64501-z$$gVol. 16, no. 1, p. 8774$$n1$$p8774$$tNature Communications$$v16$$x2041-1723$$y2025
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