PXD070243-1

PXD070243 is an original dataset announced via ProteomeXchange.

Title	Comparative Evaluation of Solid-Phase and Membrane Mimetic Strategies in Membrane Proteome Coverage and Disease-State Analysis
Description	Membrane proteins (MPs) are vital to cellular signaling, metabolism, and disease pathology, yet remain underrepresented in proteomics. To address this, several independent workflows have been developed to enable the profiling of the membrane proteome, however the relative advantages and limitations of each method remains poorly defined. Here, we systematically compare four classical solid-phase membrane proteomic workflows (SP3, SP4, FASP, S-Trap) and three membrane mimetic strategies (Peptidisc, nanodisc, and SMALP copolymer) for mass spectrometry-based membrane proteome profiling, using healthy (LFD) and obese (HFD) mouse liver tissue. We found that the solid-phase methods yield higher total protein identifications, while the membrane mimetic systems enrich MPs. SMALP copolymer displays intermediate characteristics between the solid-phase and membrane mimetic workflows. Peptidisc and nanodisc stand out for their enrichment of MPs, although Peptidisc shows better enrichment of plasma membrane integral MPs, particularly those with 11+ transmembrane segments. In the context of HFD-induced liver proteome remodeling, the Peptidisc workflow outperformed the other six methods by capturing the highest number of differentially expressed MPs and demonstrating the lowest standard deviation of MP-level dysregulation. Collectively, this comparative analysis highlights the trade-offs between depth of proteome coverage and MP enrichment across workflows, underscoring the importance of method selection based on total protein counts, MP enrichment, and the accurate detection of MP-level dysregulation.
HostingRepository	PRIDE
AnnounceDate	2026-01-01
AnnouncementXML	Submission_2026-01-01_13:08:01.297.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ashim Bhattacharya
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-03 13:07:47	ID requested
⏵ 1	2026-01-01 13:08:02	announced

10.1016/j.mcpro.2025.101496;

Antony F, Bhattacharya A, Aoki H, Jandu RS, Abdualkader AM, Al Batran R, Babu M, Duong van Hoa F, Comparative Evaluation of Solid-phase and Membrane Mimetic Strategies in Membrane Proteome Coverage and Disease-State Analysis. Mol Cell Proteomics, 25(2):101496(2025) [pubmed]

submitter keyword: Membrane Proteomics, Membrane Mimetics, Disease-State Analysis

Dr. Franck Duong
contact affiliation	University of British Columbia Faculty of Medicine Department of Biochemistry and Molecular Biology
contact email	fduong@mail.ubc.ca
lab head
Ashim Bhattacharya
contact affiliation	University of British Columbia
contact email	ashim938@student.ubc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD070243
     1. Label: PRIDE project
     2. Name: Comparative Evaluation of Solid-Phase and Membrane Mimetic Strategies in Membrane Proteome Coverage and Disease-State Analysis