Gas-phase fractionation DDA promotes in-depth DIA phosphoproteome analysis.

Zhiwei Tu, Yabin Li, Shuhui Ji, Shanshan Wang, Rui Zhou, Gertjan Kramer, Yu Cui, Fei Xie

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Article in Heliyon, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

8 authors.

Zhiwei TuState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China.

Yabin LiCollege of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, 100048, Beijing, China.

Shuhui JiState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China.

Shanshan WangState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China.

Rui ZhouThe First Affiliated Hospital of Henan University of Chinese Medicine, 450000, Zhengzhou, Henan, China.

Gertjan KramerLaboratory for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.

Yu CuiState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China.

Fei XieCollege of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, 100048, Beijing, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Data-independent acquisition (DIA) is a promising method for quantitative proteomics. Library-based DIA database searching against project-specific data-dependent acquisition (DDA) spectral libraries is the gold standard. These libraries are constructed using material-consuming pre-fractionation two dimensional DDA analysis. The alternative to this is library-free DIA analysis. Limited sample amounts restrict the use of fractionation to build spectral libraries for post-translational modifications (PTMs) DIA analysis. We present the use of gas-phase fractionation (GPF) DDA data to improve the depth of library-free DIA identification for the phosphoproteome, called GPF-DDA hybrid DIA. This method fully utilizes the remnants of samples post-DIA analysis and leverages both library-based and -free DIA database searching. GPF-DDA hybrid DIA analyzes phosphopeptides surplus sample after DIA analysis using a number of DDA injections with each scanning different mass-to-charge (

Indexed as

ARDS/ALIDIAGas phase fractionationGPF DDAPhosphoproteome

Identifiers

PMID39897833

DOI10.1016/j.heliyon.2025.e41928

PMCPMC11787513

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.