YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

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.

Rapid discovery and identification of 68 compounds in the active fraction from Xiao-Xu-Ming decoction(XXMD) by HPLC-HRMS and MTSF technique

Xiao-Xu-Ming decoction（XXMD） was a traditional Chinese prescription and first recorded in ＂Bei Ji Qian Jin Yao Fang＂.It has been widely used to treat theoplegia and the sequel of theoplegia in China.In the present work,high-performance liquid chromatography coupled with high resolution mass spectrometry（HPLC-HRMS） combined with the mass spectral tree similarity filter technique（MTSF）was used to rapidly discover and identify the compounds of the active fraction of XXMD.A total of 3362 compounds were automatically detected by HPLC-HRMS,and final 68 compounds were identified in the active fraction of XXMD.including 14 templated compounds（reference compounds）,50 related compounds fished by MTSF technique,and 4 unrelated compounds identified by manual method.This study successfully applied MTSF technology for the first time to discover and identify the components of Chinese prescription.The results demonstrated that MTSF technique should be useful to the discovery and identification of compounds in Chinese prescription.This study also proved that MTSF can be applied to the targeted phytochemical separation.