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Mass spectrometry proteomics and glycoproteomics data from human body fluids

ABSTRACT: The study of proteins and N-glycosylation in human body fluids (HBFs) is crucial for understanding both physiological and pathological states, offering valuable insights for disease diagnostics and monitoring. In this study, we present a comprehensive proteomics and glycoproteomics dataset featuring 15 types of HBFs (plasma (P), urine (U), cerebrospinal fluid (CSF), pleural fluid (PF), ascitic fluid (AF), synovial fluid (SF), pericardial fluid (PCF), peritoneal dialysis effluent (PDE), bile (B), gastric juice (GJ), seminal plasma (SP), saliva (SA), pancreatic juice (PJ), sweat (SW), and tear (T)). We also provide detailed protocols for protein processing specific to each type of HBF. The re sulting peptides and enriched intact N-glycopeptides were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data independent acquisition (DIA) and combined electron transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation (EThcD-sceHCD) mode, respectively. The resulting spectra and searched files have been uploaded to online repository iProX (www.iprox.cn) and made easily accessible to facilitate further research into HBF proteomics and glycoproteomics.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yong Zhang

PROVIDER: PXD068799 | iProX | Thu Sep 25 00:00:00 BST 2025

REPOSITORIES: iProX

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Project description:To examine the effect of seminal fluid on the whole genome expression profile of endometrial tissue following mating, RNA was extracted from endometrial tissue collected 8 h after CBAF1 females were mated with intact Balb/c males and compared to RNA from endometrial tissue of females mated with seminal fluid deficient SVX/VAS Balb/c males. This comparison controlled for ovarian hormone status, exposure to the male and mating activity, and the neuroendocrine response to cervical and vaginal stimulus at mating, so that changes in endometrial gene expression could be attributed specifically to contact with seminal fluid. The endometrial RNA from n=16 individual females was pooled into four independent biological replicates per treatment group (n=4 endometrial samples per replicate) and expression profiles were analyzed by Affymetrix microarray. Seminal fluid exposure induced a clear difference in the profile of genes expressed in the endometrium with a total of 335 genes were differentially regulated with a fold-change greater than 1.5 and p<0.05. Of these, 190 genes were upregulated and 145 genes were downregulated following contact with seminal fluid. Bioinformatics analysis revealed TLR4 signaling as a strongly predicted upstream regulator activated by the differentially expressed genes.Additional experiments confirmed the role of TLR4 with the absence of TLR4 in TLR4 null mice resulting in a failure for seminal fluid to induce endometrial Csf3, Cxcl2, Il6 and Tnf expression. This study provides evidence that TLR4 contributes to seminal fluid modulation of the periconception immune environment. Activation of TLR4 signaling by microbial or endogenous components of seminal fluid is thus implicated as a key element of the female tract response to seminal fluid at the outset of pregnancy in mice. Endometrial RNA collected 8 h following coitus from n=16 individual females was pooled into four independent biological replicates per treatment group (n=4 endometrial samples per replicate) and expression profiles were analyzed by Affymetrix microarray. Microarray analysis was performed using Affymetrix Mouse Gene 2.0 ST Arrays at the Adelaide Microarray Centre (Adelaide, Australia). Total RNA (300 ng) was labelled using the GeneChip® WT PLUS Reagent Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA). Microarray data was analyzed using Partek Genomics Suite version 6.6). Briefly, .cel files were imported using RMA background correction, following GC content correction and mean probe summarization. Differentially expressed probes were defined as ≥1.50-fold change, t-test p <0.05. To investigate gene pathways and upstream regulators activated by seminal fluid following mating, differentially expressed genes were analyzed using Ingenuity Pathway Analysis (IPA) version 18488943 Build 308606M (IPA, Ingenuity Systems, Redwood City, CA).

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Mass spectrometry proteomics and glycoproteomics data from human body fluids

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