Accurate characterization of the chemical composition of complex traditional Chinese medicine(TCM)is an essential foundation for the modern scientific interpretation of TCM principles.Mass spectrometry is the most dom...Accurate characterization of the chemical composition of complex traditional Chinese medicine(TCM)is an essential foundation for the modern scientific interpretation of TCM principles.Mass spectrometry is the most dominant technique in current research on the material basis of TCM,offering the highest sensitivity and the richest information provision.Establishing mass spectrometry databases represents the most effective approach to facilitating the structural analysis of TCM chemical components.This paper systematically searches and reviews literature published from January 2005 to January 2025 through online databases such as China National Knowledge Infrastructure,PubMed,and Web of Science,using“mass spectrometry database”and“traditional Chinese medicine”as keywords.It reviews the current status of seven TCM chemical component mass spectrometry databases and seven natural product mass spectrometry databases.The key advancements of these mass spectrometry databases for natural products are summarized,detailing their characteristics,search methodologies,included information,and data sources.Additionally,challenges related to data quality,standardization,timely updates,database interaction,retrieval functionality,and data sharing and security are discussed in depth.Furthermore,the paper explores prospective development directions for TCM mass spectrometry databases,emphasizing the importance of open data sharing,technological innovation,and data security.Through this analysis,the paper aims to offer theoretical guidance and practical recommendations for the precise identification of TCM components,as well as for the construction and application of these databases.展开更多
In this paper,we report the construction of two accurate mass databases and the development of a combination detection method that simultaneously screens for 733 pesticide and chemical contaminant multi-residues via h...In this paper,we report the construction of two accurate mass databases and the development of a combination detection method that simultaneously screens for 733 pesticide and chemical contaminant multi-residues via high-throughput liquid chromatography(LC)-and gas chromatography(GC)-quadru pole-time-of-flight mass spectrometry(Q-TOFMS).This work demonstrates that electronic mass spectral standards may replace chemical-source standard materials as references through one sample preparation and the combination of GC/LC-Q-TOFMS screening.This cutting-edge technique has also replaced multiresidue determination using targeted detection with non-targeted screening.The pesticide residue types,sensitivity,recovery,and reproducibility of this combination technique are evaluated in eight fruit and vegetable matrices.This technique shows three advantages:①In comparison with the discovery capability of a single technique,the combination technique shows an improvement of 51.1%(GC-QTOFMS)and 39.6%(LC-Q-TOFMS),respectively;②the combination technique can satisfy a screening limit lower than 10μg·kg^-1 and meet the requirements of“uniform standards,”although some of the pesticide residues could be optimized to further improve screening sensitivity;③over 488 pesticides with recoveries between 60%-120%and relative standard deviation(RSD)<20%at a spiked level of 10μg·kg^-1 were detected with the combination technique in eight different matrices.From 2012 to 2017,this combination technique was applied in an investigation to screen pesticide residues from 1384 sampling locations for 38138 batched samples covering 18 categories and 134 types of fruits and vegetables obtained from across the mainland of China.After statistical analysis,533 pesticides in 115891 determinations were detected,and the regularity of pesticides in the fruits and vegetables sold on the Chinese market was shown.展开更多
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED ...We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.展开更多
基金the Beijing Natural Science Foundation(No.7252249)the National Natural Science Foundation of China(No.82104380)+1 种基金the Scientific and Technological Innovation Project of the China Academy of Chinese Medical Sciences(Nos.CI2023E002,CI2023C071YLL, CI2023C039YGL)the Fundamental Research Funds for the Central Public Welfare Research Institutes(No.ZZ14-YQ-047, ZZ15-WT-04)。
文摘Accurate characterization of the chemical composition of complex traditional Chinese medicine(TCM)is an essential foundation for the modern scientific interpretation of TCM principles.Mass spectrometry is the most dominant technique in current research on the material basis of TCM,offering the highest sensitivity and the richest information provision.Establishing mass spectrometry databases represents the most effective approach to facilitating the structural analysis of TCM chemical components.This paper systematically searches and reviews literature published from January 2005 to January 2025 through online databases such as China National Knowledge Infrastructure,PubMed,and Web of Science,using“mass spectrometry database”and“traditional Chinese medicine”as keywords.It reviews the current status of seven TCM chemical component mass spectrometry databases and seven natural product mass spectrometry databases.The key advancements of these mass spectrometry databases for natural products are summarized,detailing their characteristics,search methodologies,included information,and data sources.Additionally,challenges related to data quality,standardization,timely updates,database interaction,retrieval functionality,and data sharing and security are discussed in depth.Furthermore,the paper explores prospective development directions for TCM mass spectrometry databases,emphasizing the importance of open data sharing,technological innovation,and data security.Through this analysis,the paper aims to offer theoretical guidance and practical recommendations for the precise identification of TCM components,as well as for the construction and application of these databases.
基金financial support of the National Key Technology Research and Development Program(2012BAD29B01)the Key Basic Research Program(2015FY111200)of the Ministry of Science and Technology,China.
文摘In this paper,we report the construction of two accurate mass databases and the development of a combination detection method that simultaneously screens for 733 pesticide and chemical contaminant multi-residues via high-throughput liquid chromatography(LC)-and gas chromatography(GC)-quadru pole-time-of-flight mass spectrometry(Q-TOFMS).This work demonstrates that electronic mass spectral standards may replace chemical-source standard materials as references through one sample preparation and the combination of GC/LC-Q-TOFMS screening.This cutting-edge technique has also replaced multiresidue determination using targeted detection with non-targeted screening.The pesticide residue types,sensitivity,recovery,and reproducibility of this combination technique are evaluated in eight fruit and vegetable matrices.This technique shows three advantages:①In comparison with the discovery capability of a single technique,the combination technique shows an improvement of 51.1%(GC-QTOFMS)and 39.6%(LC-Q-TOFMS),respectively;②the combination technique can satisfy a screening limit lower than 10μg·kg^-1 and meet the requirements of“uniform standards,”although some of the pesticide residues could be optimized to further improve screening sensitivity;③over 488 pesticides with recoveries between 60%-120%and relative standard deviation(RSD)<20%at a spiked level of 10μg·kg^-1 were detected with the combination technique in eight different matrices.From 2012 to 2017,this combination technique was applied in an investigation to screen pesticide residues from 1384 sampling locations for 38138 batched samples covering 18 categories and 134 types of fruits and vegetables obtained from across the mainland of China.After statistical analysis,533 pesticides in 115891 determinations were detected,and the regularity of pesticides in the fruits and vegetables sold on the Chinese market was shown.
基金supported in part by the National Institutes of Health of the United States(Grant Nos.UL1 RR024139 to Yale Clinical and Translational Science Award,1S10OD018034-01 to 6500 QTrap Mass Spectrometer for Yale University,1S10RR026707-01 to 5500QTrap Mass Spectrometer for Yale University,P30DA018343 to Yale/NIDA Neuroproteomics Center and NIDDK-K01DK089006 awarded to JR)
文摘We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
