Monitoring proteome dynamics from different human cell types present concomitantly in a given sample is of great interest and could be applied to ultra-precise molecular characterization of complex tissues. Here, we propose a proteogenomics-based strategy to point at cell line molecular signatures. For this, the proteome is analyzed by high-throughput shotgun mass spectrometry and specific bioinformatics search are performed. First, mRNA from chondrosarcoma cells (SW1353 cell line) and immortalized chondrocytes (T/C28A2 cell line) were sequenced by RNAseq for establishing the most appropriate protein sequence database. For this an innovative cascade search allows to conciliate de novo and mapping RNAseq assemblies and the Human swissprot databases (Cogne et al., 2018). A set of 2 million of discriminating peptide sequences of the two cell lines are then identified. From them, 480 peptide sequences were detected and monitored based on extracted ion chromatogram (XIC) signals recorded by tandem mass spectrometry. A list of 55 peptides were used for quantitating the ratio of each cell type in a given co-culture sample with high precision selected with cell lines mixed at 2:1, 1:1; and 1:2 ratio. This new methodology was used to analyze the bystander effect generated by irradiated chondrosarcoma cells (SW1353 cell line) on immortalized chondrocytes (T/C28A2 cell line) in co-culture conditions. Such strategy could be applied to investigate intercellular interactions between different cell types, paving the way to new insights into the molecular mechanisms of crosstalk between human cells.