Objective To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain. Methods We developed a JAVA program for searching sho...Objective To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain. Methods We developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini, which PDZ domains recognized experimentally, Swissprot database has been searched by this program for all potential ligands. Results Some PDZ domains may have more potential ligand proteins, which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains’ protein interactions in many different organisms. Conclusion The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.展开更多
Objective To estimate the effect of two simple filters, two or more positive peptide filter and Unified Score filter on the true positive rate of protein and peptide. Methods Twenty-two LC-MS/MS datasets were from 18 ...Objective To estimate the effect of two simple filters, two or more positive peptide filter and Unified Score filter on the true positive rate of protein and peptide. Methods Twenty-two LC-MS/MS datasets were from 18 known protein mixture. Two or more positive peptide filter and Unified Score filter were applied to the 22 datasets. The filters effect was evaluated according to the true positive rate of protein and peptide for each filter. Results The positive rates of protein and peptide from two or more peptide filter raised from 56.49% to 92.86%-99.12% (for protein) and from 90.67% to 97.74%-99.62% (for peptide), but many positive proteins were filtered out. The positive rates of protein and peptide from Unified Score (ThermoFinnigan value 2400) were only about 35.51% and 82.99%, but after adjusted the value (3900) according to the number of false positive peptide, those positive rate raised to 63.61% (for protein) and 91.97% (for peptide). Conclusions Two or more peptides requirement could significantly decrease false positive rate, but it also may filter out many true positive proteins especially low molecular weight and less abundant proteins. Unified Score may be a better filter than Xcorr and DeltaCn combination and the value of 3900 is found to be more suitable for this particular datasets.展开更多
In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identi?ed peptides in reverse phase liquid chromatogra- phy and electrospray tandem mass spectrometry (RPLC...In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identi?ed peptides in reverse phase liquid chromatogra- phy and electrospray tandem mass spectrometry (RPLC-MS/MS) analysis. Fol- lowing protein digestion with trypsin, the peptide mixture was analyzed by on-line RPLC-MS/MS. Bovine serum albumin (BSA) was used to optimize acetonitrile (ACN) elution gradient for tryptic peptides, and Cytochrome C was used to retest the gradient and the sensitivity of LC-MS/MS. The characteristics of identi?ed peptides were also analyzed. In our experiments, the suitable ACN gradient is 5% to 30% for tryptic peptide elution and the sensitivity of LC-MS/MS is 50 fmol. Analysis of the tryptic peptides demonstrated that longer (more than 10 amino acids) and multi-charge state (+2, +3) peptides are likely to be identi?ed, and the hydropathicity of the peptides might not be related to whether it is more likely to be identi?ed or not. The number of identi?ed peptides for a protein might be used to estimate its loading amount under the same sample background. Moreover, in this study the identi?ed peptides present three types of redundancy, namely iden- ti?cation, charge, and sequence redundancy, which may repress low abundance protein identi?cation.展开更多
Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 ...Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree wasgenerated. In this tree, proteins with similar known function were classified into the same group.Some proteins in the same group have been reported to have similar binding motifs experimentally.The tree might provide clues about possible functions of hypothetical proteins for furtherexperimental verification.展开更多
基金Supported by the National Natural Sciences Foundation of China(General Program: 3037030 30270657 and Key Program: 30230150) Early Phase Study Supported by the Key Basic Research Project (2002-CCA04100) the National High Technology Research and Devel
文摘Objective To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain. Methods We developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini, which PDZ domains recognized experimentally, Swissprot database has been searched by this program for all potential ligands. Results Some PDZ domains may have more potential ligand proteins, which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains’ protein interactions in many different organisms. Conclusion The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.
基金Supported by grants from the National Basic Research Program (973)2004CB520804 ,National Natural Science Foundation of China (30270657,30230150 ,3037030 ).
文摘Objective To estimate the effect of two simple filters, two or more positive peptide filter and Unified Score filter on the true positive rate of protein and peptide. Methods Twenty-two LC-MS/MS datasets were from 18 known protein mixture. Two or more positive peptide filter and Unified Score filter were applied to the 22 datasets. The filters effect was evaluated according to the true positive rate of protein and peptide for each filter. Results The positive rates of protein and peptide from two or more peptide filter raised from 56.49% to 92.86%-99.12% (for protein) and from 90.67% to 97.74%-99.62% (for peptide), but many positive proteins were filtered out. The positive rates of protein and peptide from Unified Score (ThermoFinnigan value 2400) were only about 35.51% and 82.99%, but after adjusted the value (3900) according to the number of false positive peptide, those positive rate raised to 63.61% (for protein) and 91.97% (for peptide). Conclusions Two or more peptides requirement could significantly decrease false positive rate, but it also may filter out many true positive proteins especially low molecular weight and less abundant proteins. Unified Score may be a better filter than Xcorr and DeltaCn combination and the value of 3900 is found to be more suitable for this particular datasets.
基金This work was partially supported by grants fromthe National Basic Research Program (973) of China(2004CB520804), and National Natural Science Foun-dation of China (No. 30270657, 30230150, 3037030).
文摘In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identi?ed peptides in reverse phase liquid chromatogra- phy and electrospray tandem mass spectrometry (RPLC-MS/MS) analysis. Fol- lowing protein digestion with trypsin, the peptide mixture was analyzed by on-line RPLC-MS/MS. Bovine serum albumin (BSA) was used to optimize acetonitrile (ACN) elution gradient for tryptic peptides, and Cytochrome C was used to retest the gradient and the sensitivity of LC-MS/MS. The characteristics of identi?ed peptides were also analyzed. In our experiments, the suitable ACN gradient is 5% to 30% for tryptic peptide elution and the sensitivity of LC-MS/MS is 50 fmol. Analysis of the tryptic peptides demonstrated that longer (more than 10 amino acids) and multi-charge state (+2, +3) peptides are likely to be identi?ed, and the hydropathicity of the peptides might not be related to whether it is more likely to be identi?ed or not. The number of identi?ed peptides for a protein might be used to estimate its loading amount under the same sample background. Moreover, in this study the identi?ed peptides present three types of redundancy, namely iden- ti?cation, charge, and sequence redundancy, which may repress low abundance protein identi?cation.
基金This work was partly supported by grants from Na-tional Natural Science Foundation of China (No.3037030 30270657 and 30230150)+2 种基金 Major State Basic Research Development Program of China(2004CB520804) Pilot Study for Key Basic Re-search Project of China (2002CCA04100) and Key Project for International Cooperation of China (2002AA229031).
文摘Domain database is essential for domain property research. Eliminatingredundant information in database query is very important for database quality. Here we report themanual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree wasgenerated. In this tree, proteins with similar known function were classified into the same group.Some proteins in the same group have been reported to have similar binding motifs experimentally.The tree might provide clues about possible functions of hypothetical proteins for furtherexperimental verification.
