Proteomic investigation of smooth muscle cells under PDGF/L1B vs.TGB1 stimulation

Human aortic smooth muscel cells (Thermo Fisher Scientific, C-007-5C, LOT: 2164581) were treated with TGB1 or PDGF/L1B to induce the contractile or synthetic SMC phenotype. As part of a multi-omics analysis, we conducted mass spectrometry to quantify protein levels of cell lysates using a HPLC-ESI-MS/MS system (HPLC=high pressure liquid chromatography, Ultimate 3000 UPLC system; ESI=electrospray ionization) and an Orbitrap Exploris™ 480 mass spectrometer. MS data were analyzed and normalized with the Spectronaut software (https://biognosys.com/software/spectronaut/) using the Uniprot fasta reference (human_uniprot_swissprot_2023_12.fasta). In total, 4993 proteins were identified with a minimum of two peptide per protein. Only unique and razor peptides were considered. The statistical analysis was performed on peptide level using the PECA package (version: 1.40.0, DOI: 10.18129/B9.bioc.PECA). A ROTS test (ROPECA approach - reproducibility-optimized peptide change averaging) implemented in the PECA package (DOI: 10.1371/journal.pcbi.1005562).