Multi-omics exploration on polystyrene microplastic effects on term placental explants - Proteomics Raw Data

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.