PXD070887

PXD070887 is an original dataset announced via ProteomeXchange.

Title	Label-free DIA proteomics of WT, HET, and SMA mouse liver at postnatal day 10 (P10)
Description	This dataset contains label-free DIA proteomics of liver tissue from postnatal day 10 (P10) Taiwanese SMA mice (genotype: Smn−/−; SMN2tg/0), heterozygous carriers (HET, Smn+/−; SMN2tg/0), and wild-type controls (WT, Smn+/+; SMN2 0/0). SMA and HET samples were littermates generated from the same FVB/N × C57BL/6 mixed-background colony, whereas WT controls were age-matched animals on a C57BL/6 background. Whole-liver lysates were processed by in-solution protein digestion and analyzed using data-independent acquisition (DIA) LC–MS/MS on a Thermo Orbitrap Exploris 480 mass spectrometer equipped with a FAIMS Pro differential ion mobility device. A Vanquish Neo nano-HPLC system (Thermo Scientific) was coupled to the mass spectrometer for chromatographic separation. Peptide and protein identification and quantification were performed with DIA-NN v1.8.1using a predicted spectral library generated from the Mus musculus UniProt canonical FASTA file (accession UP000000589, downloaded 2024-01-04). The DIA-NN output was filtered at 1% precursor- and protein-level FDR (global q-value ≤ 0.01), with additional quality filters applied in R (≥ 4 fragment ions per precursor, library q-value ≤ 0.01, unique peptides only). Final LFQ intensities were calculated using the DIA-NN R package, and downstream statistical analysis was performed in Perseus v1.6.15. All RAW files generated during data acquisition are included in this dataset. One SMA biological replicate was identified as an outlier by principal component analysis and excluded from downstream statistical comparisons in the accompanying manuscripts: this corresponds to SMN biological replicate 5 (Raw file: E3_CoIID_656_3632_LI_165). Its RAW file and corresponding DIA-NN output tables are provided here for completeness, transparency, and reproducibility. The dataset contains the original RAW files, DIA-NN search output tables (.tsv), the predicted spectral library used for identification, and the Mus musculus UniProt FASTA database employed for database searching. Experimental factors encoded in the metadata include genotype (WT, HET, SMA) and tissue (liver).
HostingRepository	PRIDE
AnnounceDate	2026-01-11
AnnouncementXML	Submission_2026-01-11_13:05:47.957.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	SOFIA VRETTOU
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-18 06:07:18	ID requested
⏵ 1	2026-01-11 13:05:48	announced

10.64898/2026.01.08.698518;

submitter keyword: P10, mouse model, proteomics, DIA-NN, DIA, SMA, liver, HET, label-free quantification, label-free, WT,Spinal muscular atrophy

Brunhilde Wirth
contact affiliation	Director & Chair Institute of Human Genetics University Hospital Cologne Kerpener Str. 34 50931 Cologne Germany
contact email	brunhilde.wirth@uk-koeln.de
lab head
SOFIA VRETTOU
contact affiliation	Institute of Human Genetics, Center for Molecular Medicine Cologne, University Hospital of Cologne, University of Cologne
contact email	sofia.vrettou@uk-koeln.de
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/2026/01/PXD070887

PRIDE project URI

• PRIDE
  1. PXD070887
     1. Label: PRIDE project
     2. Name: Label-free DIA proteomics of WT, HET, and SMA mouse liver at postnatal day 10 (P10)