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Multi-omics exploration on polystyrene microplastic effects on term placental explants - Proteomics Raw Data
Summary
Scientists exposed pieces of real human placenta tissue to microplastics (tiny plastic particles) in the lab, then used advanced protein-analysis technology to see how thousands of placental proteins changed in response. This study focused on generating and sharing the detailed protein data itself, laying groundwork for future research into whether microplastic exposure during pregnancy could affect placental function and, potentially, fetal health.
Global proteomic profiling was performed on human placental explants using a single-pot solid-phase-enhanced sample preparation (SP3) workflow followed by data-independent acquisition parallel accumulation–serial fragmentation (DIA-PASEF) on a timsTOF HT mass spectrometer coupled to a nanoElute LC system. Protein identification and quantification were carried out with DIA-NN v2.1.0 against the human reference proteome, using a 1% false discovery rate (FDR), allowing up to two missed cleavages, with carbamidomethylation (Cys) as a fixed modification and methionine oxidation as a variable modification. Match-between-runs was enabled to improve protein quantification across samples. After quality control, samples with insufficient protein yield were excluded, resulting in 6 control, 7 PS1, and 8 PS100 samples. Protein intensities were log-transformed and constant median normalized prior to statistical analysis. Two complementary analysis pipelines were employed: (i) filtering proteins with fewer than five valid values per group followed by missing-value imputation in Perseus, and (ii) analysis of the complete dataset without filtering or imputation. Downstream statistical analyses and visualization were performed in R using in-house scripts together with the ropls, ggpubr, rstatix, ComplexHeatmap, and EnhancedVolcano packages.