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
Following the completion of genome sequencing of model plants,such as rice(Oryza sativa L.)and Arabidopsis thaliana,the era of functional plant genomics has arrived which provides a solid basis for the develop-ment of...Following the completion of genome sequencing of model plants,such as rice(Oryza sativa L.)and Arabidopsis thaliana,the era of functional plant genomics has arrived which provides a solid basis for the develop-ment of plant proteomics.We review the background and concepts of proteomics,as well as the key techniques which include:(1)separation techniques such as 2-DE(two-dimensional electrophoresis),RP-HPLC(reverse phase high performance liquid chromatography)and SELDI(surface enhanced laser desorption/ionization)protein chip;(2)mass spectrometry such as MALDI-TOF-MS(matrix assisted laser desorption/ionization-time of flight-mass spectrometry)and ESI-MS/MS(electrospray ionization mass spectrometry/mass spectrometry);(3)Peptide sequence tags;(4)databases related to proteomics;(5)quantitative proteome;(6)TAP(tandem affinity purification)and(7)yeast two-hybrid system.In addition,the challenges and prospects of pro-teomics are also discussed.展开更多
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.
文摘Following the completion of genome sequencing of model plants,such as rice(Oryza sativa L.)and Arabidopsis thaliana,the era of functional plant genomics has arrived which provides a solid basis for the develop-ment of plant proteomics.We review the background and concepts of proteomics,as well as the key techniques which include:(1)separation techniques such as 2-DE(two-dimensional electrophoresis),RP-HPLC(reverse phase high performance liquid chromatography)and SELDI(surface enhanced laser desorption/ionization)protein chip;(2)mass spectrometry such as MALDI-TOF-MS(matrix assisted laser desorption/ionization-time of flight-mass spectrometry)and ESI-MS/MS(electrospray ionization mass spectrometry/mass spectrometry);(3)Peptide sequence tags;(4)databases related to proteomics;(5)quantitative proteome;(6)TAP(tandem affinity purification)and(7)yeast two-hybrid system.In addition,the challenges and prospects of pro-teomics are also discussed.
