PXD076278

PXD076278 is an original dataset announced via ProteomeXchange.

Title	A Tiered Approach to Human Synapse Proteomics: Optimized LC-MS/MS Analysis of Whole-Tissue Lysate and Synaptosome Preparations from Frozen Post-Mortem Brain Samples
Description	Recent advancements in neuroproteomics have enabled detailed analysis of protein expression and function in the human brain, improving our understanding of the relationship between genetics, cell biology of neurological and psychiatric disorders and their clinical diagnosis. Synaptic dysfunction often has a central role in these disorders. Leveraging the high sensitivity of modern liquid chromatography-tandem mass spectrometry (LC-MS/MS), we here evaluated the detection of synaptic proteins in whole-tissue lysates compared to enriched synaptosome preparations. First, we optimized sample preparation protocols for frozen human gray matter (GM), refining the suspension TRAPping (sTRAP) digestion method to improve protein solubilization and Cysteine reduction and alkylation using thin human tissue sections, and to accomplish low technical variation by minimizing sample handling. We achieved a highly reproducible sample preparation workflow by rigorously applying standardization and randomization across dissection, processing, and LC-MS/MS runs. Second, comparative LC-MS/MS analysis showed that cortical whole-tissue lysates are a practical solution for large-scale studies and broadly detected synaptic proteins. However, synaptosome isolation offered improved resolution of synapse-specific proteins. Because synapse-proteomics enables insight into spatial regulation—i.e., alterations at the synapse not reflected in the soma– we recommend a tiered approach for large-scale studies: initial whole-tissue lysate analysis for broad disease-associated changes, followed by targeted synaptosome proteomics to deepen insight into synaptic alterations. This strategy optimally balances throughput, reproducibility, and biological relevance, and enhances the study of brain disorders through proteomics. Moreover, analyzing synaptic proteins first at the tissue level improves insight into overall regulation of synaptic proteins induced by synapse loss or gain.
HostingRepository	PRIDE
AnnounceDate	2026-05-25
AnnouncementXML	Submission_2026-05-24_16:15:06.780.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Remco Klaassen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2; timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-27 17:43:15	ID requested
⏵ 1	2026-05-24 16:15:07	announced

10.3390/cells15080736;

Roig-Kuhn FC, Klaassen RV, Koopmans FTW, Koolman TSZ, Smit AB, Spijker S, A Tiered Approach to Human Synapse Proteomics: Optimized LC-MS/MS Analysis of Whole-Tissue Lysate and Synaptosome Preparations from Frozen Post-Mortem Brain Samples. Cells, 15(8):(2026) [pubmed]

submitter keyword: None

Sabine Spijker
contact affiliation	Dept. of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
contact email	s.spijker@vu.nl
lab head
Remco Klaassen
contact affiliation	Department of Molecular and Cellular Neurobiology. Vrije Universiteit Amsterdam.
contact email	r.v.klaassen@vu.nl
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/2026/05/PXD076278

PRIDE project URI

• PRIDE
  1. PXD076278
     1. Label: PRIDE project
     2. Name: A Tiered Approach to Human Synapse Proteomics: Optimized LC-MS/MS Analysis of Whole-Tissue Lysate and Synaptosome Preparations from Frozen Post-Mortem Brain Samples