PXD063082-1

PXD063082 is an original dataset announced via ProteomeXchange.

Title	Localisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)
Description	Subcellular localisation within the proteome fundamentally influences cellular processes, however the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping with in-depth subcellular resolution. This unified framework integrates differential-ultracentrifugation with ion-mobility-based data independent acquisition (DIA) mass spectrometry, alongside data processing using DIA-NN and spatial analysis within the pRoloc bioinformatics pipeline. Within the same experimental pipeline, we compare Differential-ultraCentrifugation (DC) fractionation with an alternate detergent-based protocol using both data-dependent (DDA) and data-independent acquisition (DIA) mass spectrometry approaches highlighting the increased subcellular resolution of the DC approach and the increased proteome coverage when DIA is applied. This study thus informs potential users of subcellular proteomics strategies that employ biochemical fractionation of the optimal workflows to achieve high proteome coverage and subcellular resolution.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-29_15:42:26.494.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kieran McCaskie
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-17 13:23:29	ID requested
⏵ 1	2025-09-29 15:42:27	announced

McCaskie K, Hutchings C, Feret R, Kim YI, Breckels L, Deery M, Lilley K, Localization of Organelle Proteins Using Data-Independent Acquisition (DIA-LOP). Mol Cell Proteomics, 24(9):101047(2025) [pubmed]

10.1016/j.mcpro.2025.101047;

submitter keyword: Human, LC-MSMS, DIA, diaPASEF, DDA

Kathryn S. Lilley
contact affiliation	Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
contact email	ksl23@cam.ac.uk
lab head
Kieran McCaskie
contact affiliation	University of Cambridge
contact email	km853@cam.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063082
     1. Label: PRIDE project
     2. Name: Localisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)