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This figure presents Atlas, a mass spectrometry processing pipeline built with Nextflow. It handles both DDA and DIA data through different paths: raw spectral data is parsed, followed by peptide and protein identification using either FragPipe (DDA) or DIA-NN (DIA). The organism-specific FASTA file guides this identification process. Finally, QSample computes quality control metrics and generates visual outputs, ensuring reliable and streamlined proteomic analysis.