Umami peptides screened based on peptidomics and virtual screening from Ruditapes philippinarum and Mactra veneriformis clams

Umami is the fifth taste found in substances that mainly include amino acids and nucleotides. Past studies have focused on umami peptides in meat and vegetables, however, recently umami peptides were also reported in seafood. Separation methods commonly used for umami peptides from foods are laborious and time consuming. In this paper, the combination of peptidomics and virtual screening is employed for rapid screening of samples with high efficiency. Virtual screening is a computational technique combining bioinformatics, molecular docking, and large datasets to identify potential hit candidates.

Mactra veneriformis and Ruditapes philippinarum (low-value shellfish widely found in China) were chosen for this study as they contain a rich source of protein. In addition to studying the umami peptides, the binding mechanisms of the peptides to the receptor T1R1/T1R3 were also investigated. Following separation, data analysis was performed using PEAKS studio. The researchers found 16 out of 18 potential candidates showed umami taste, with an accuracy of screening of 88.9%. The combination of these results and the molecular docking results revealed that hydrogen bonding is responsible for interaction of peptides with T1R1/T1R3 receptor. This study successfully revealed novel umami peptides. These peptides were identified using the combination of peptidomics and virtual screening, a fast-screening method that is likely to be exploited for future studies in this area.

How was PEAKS used?

PEAKS Studio 8.0 was used for analyzing tandem mass spectra. The acquired data were searched against a NCBI clam database (Ruditapes philippinarum; Mactra veneriformis). Precursor and fragment ion tolerance were set to 10 ppm and 0.02 Da, respectively. None was chosen as enzyme, no fixed modifications were selected, and methyl sulfide amino acid oxidation and N-terminal acetylation were set as variable modifications. The false discovery rate (FDR) was set <1%, and for de novo result confidence levels of more than 80% were retained. For both de novo and database search, peptides with molecular weight below 1500 Da were retained.

Zhang, Ting, et al. “Umami peptides screened based on peptidomics and virtual screening from Ruditapes philippinarum and Mactra veneriformis clams.” Food Chemistry 394 (2022): 133504. doi:10.1016/j.foodchem.2022.133504


The existing technology used for screening umami peptides is time-consuming and labor-intensive, making it difficult to meet the requirements of rapid screening of peptides. In this study, a high-throughput screening method for umami peptides was established based on peptidomics and virtual screening including the mass spectrometry, iUmami-SCM, PeptideRanker, and T1R1/T1R3 receptor. Subsequently, they were characterized and validated using sensory evaluation and electronic tongue. Results showed that 18 potential umami peptides were screened from two clams. Among them, 16 peptides had umami characteristics with thresholds range 0.123–1.481 mmol/L, and the accuracy of the screening method was about 88.9%. Additionally, active sites such as Tyr143, Gly144, Ser146, Ala145, His121, Ser123, and Glu277 may play a critical role in flavor presentation by molecular docking with T1R1/T1R3. The paper could provide a fast and reliable method for screening umami peptides as well as lay the foundation for novel strategies for evaluating umami taste.