PXD061609

PXD061609 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of over 13,000 proteins across ten mouse tissues using multi-dimensional peptide pre-fractionation
Description	Proteome-wide abundance profiling across tissues can help to provide insight into the biological mechanisms underlying tissue-specific function and potential related dysfunction and amelioration thereof. Here, we use sample multiplexing to profile the proteomes of ten diverse mouse tissues using TMTpro-based quantitative mass spectrometry. Our optimized workflow, incorporating two-dimensional peptide pre-fractionation (which included both basic pH reversed-phase and strong ion exchange chromatography) enabled the quantification of over 13,000 proteins across brain, brown fat, heart, kidney, liver, lung, skeletal muscle, spleen, ovaries, and testes. Global analysis revealed distinct proteome profiles for each tissue, with clear clustering patterns reflecting functional similarities and differences. We highlighted the abundance of numerous tissue-specific proteins, exemplified by Synapsin-1 in brain, Uncoupling protein 1 in brown fat, and Zona pellucida proteins in reproductive tissues. Gene ontologies and pathway analyses of the most relatively abundant proteins in each tissue revealed enrichment patterns consistent with known physiological functions. For instance, brain tissue showed enrichment for synaptic components and neurotransmission processes, while liver tissue was enriched for metabolic pathways. This dataset serves as a valuable resource for mapping tissue-specific protein landscapes in mammals, offering potential insights into the molecular mechanisms of tissue function.
HostingRepository	PRIDE
AnnounceDate	2025-11-18
AnnouncementXML	Submission_2025-11-18_10:03:26.672.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-08 10:43:13	ID requested
⏵ 1	2025-11-18 10:03:27	announced

Dataset with its publication pending

submitter keyword: TMTpro,Tissue-specific expression, strong anion exchange fractionation, real-time search, peptide SAX

Joao A. Paulo
contact affiliation	Department of Cell Biology Harvard Medical School Boston, MA 02115
contact email	joao_paulo@hms.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
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/2025/11/PXD061609

PRIDE project URI

• PRIDE
  1. PXD061609
     1. Label: PRIDE project
     2. Name: Proteomic profiling of over 13,000 proteins across ten mouse tissues using multi-dimensional peptide pre-fractionation