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Ganirelix, a peptide‐based drug used to treat female infertility, has been in high market demand, which attracted generic formulation. A hitherto unknown impurity of ganirelix was observed in our formulation process, which reached ~0.3% in 6 months and led to a detailed investigation of its structure. In‐depth analysis of ESI‐MS/MS data of this impurity coupled with an artificial intelligence prediction tool led to a highly unusual putative structure, that is, N‐(2‐carboxyethyl)‐ganirelix (NCE‐GA), which was authenticated by chemical synthesis from ganirelix and NMR analysis and via corroborated HPLC and MS/MS data with the formulation‐derived impurity. [ABSTRACT FROM AUTHOR]