Proteomics data-Comprehensive Investigation for Living Cells through Integration of Ramanomics and Multi-Omics Analyses

Each cell group was prepared in 200 μL tubes and washed once in PBS buffer. The cell suspension was removed, and 4 μL of DDM lysis buffer was added. The peptides obtained from DDM in-solution digestion were desalted using a trap column, subsequently separated on an analytical column, and analyzed by mass spectrometry employing an EASY 1200-QEHFX system (Thermo Fisher Scientific). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD074098. The raw data files acquired from the QEHFX system were searched using DIA-NN software with default settings. In instances where missing values occurred in all samples per cell type, these were assigned a background value of 1. Missing data imputation was then performed utilizing the Robust Sequential Imputation algorithm. The preprocessing steps were carried out using the NAguideR tool available on the ‘Wu Kong’ platform (https://wkomics.omicsolution.com/wkomics/main/). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted by the “clusterProfiler” R package (version 4.4.0).