PXD063053

PXD063053 is an original dataset announced via ProteomeXchange.

Title	Effects of fecal microbiota transplantation on sows' ovary protein expression
Description	The fecal suspension was prepared using the protocol previously described with minor optimization. Briefly, fresh feces samples were obtained from Meishan sows and were immediately homogenized in sterile and O2-free saline solution. Then fecal slurry was passed through the sterilized gauze and then a 0.224 mm stainless cell strainer to remove the particles. We used optical microscopy combined with methylene blue staining to count the live microbes in the fecal suspension. The Meishan sow’s neighbor L×Y sows received sterile saline (20 mL), sterilized fecal microbiota suspension (20 mL), low concentration fecal microbiota suspensions (107 CFU/mL, 20 mL), and high concentration fecal microbiota suspensions (108 CFU/mL, 20 mL) every other day from the age of 90 days to the age of puberty onset (about 200 days of age). Ovary tissue, plasma sample, and intestine stool were collected at terminal of the third estrus.Quantitative proteomics isobaric tags for relative and absolute quantitation (iTRAQ) were conducted to determine protein profile of ovary. After protein extraction, protein digestion, peptide labeling, and peptide fractionation, LC-MS/MS analysis was performed. For bioinformatics pipeline for data analysis, an automated software called IQuant for quantitatively analyzing the labeled peptides with isobaric tags. It integrates Mascot Percolator, a well performing machine learning method for rescoring database search results, to provide reliable significance measures. To assess the confidence of peptides, the PSMs were pre-filtered at a PSM-concentration FDR of 1%. Then based on the "simple principle" (The parsimony principle), identified peptide sequences are assembled into a set of confident proteins. To control the rate of false-positive at protein concentration, a protein FDR at 1%, which is based on Picked protein FDR strategy, will also be estimated after protein inference (Protein-concentration FDR <= 0.01). Proteins with 1.5-fold change and Q-value less than 0.05 were determined as differentially expressed protein in single replicate. Proteins with 1.5-fold change (mean value of all comparison groups) and P-value (t-test of all comparison groups) less than 0.05 were defined as differentially expressed proteins.
HostingRepository	iProX
AnnounceDate	2025-04-17
AnnouncementXML	Submission_2025-04-17_00:27:03.041.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Baoyang Xu
SpeciesList	scientific name: Sus scrofa domesticus; NCBI TaxID: 9825;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-17 00:26:46	ID requested
⏵ 1	2025-04-17 00:27:03	announced

Dataset with its publication pending

submitter keyword: Ovary, Meishan sows, Proteomics

Xianghua Yan
contact affiliation	Zhejiang University
contact email	xhyan2024@zju.edu.cn
lab head
Baoyang Xu
contact affiliation	Zhejiang A&F University
contact email	baoyangxu@zafu.edu.cn
dataset submitter

iProX dataset URI