With this research, the fields of proteomics and bioinformatics could be significantly advanced through improved data pre-processing, leading to enhanced LC-MS data quality. By effectively calibrating proteomics data, this study enables more accurate peptide and protein identification, as well as improved post-translational modification (PTM) analysis. Enhanced PTM identification rates could aid in elucidating complex biological mechanisms, paving the way for groundbreaking discoveries in biomarker identification and drug development. These advancements can lead to the development of more targeted and effective treatments, improving patient outcomes and quality of life. In the bioinformatics and proteomics communities, the developed mass calibration pipeline can be integrated in existing workflows. By increasing the accuracy of mass spectrometry data, researchers can achieve more reliable results, which is crucial for advancing our understanding of protein functions and interactions. This, in turn, facilitates the discovery of novel biomarkers and therapeutic targets, driving innovation in biomedical research. Furthermore, this research has the potential to streamline the drug discovery process in the pharmaceutical industry. By providing more accurate data on PTMs, the calibration pipeline accelerates the identification of new drug targets and the development of innovative therapeutics. Overall, the societal impact of this study spans across multiple domains, further enabling advancements in scientific knowledge and healthcare. It offers a reliable tool for more accurate PTM characterization and may enable a deeper understanding of their functional roles in biological systems. This may further drive innovation in biomedical research and ultimately contribute to the general improvement of human health.