为了有效地利用蛋白质串联质谱数据,提高蛋白质鉴定的准确性,提出了一种基于信息论的蛋白质数据库搜索鉴定算法——ITPIA(information theory based protein identification algorithm)算法.针对多肽串联质谱质量低、噪音多等问题,ITPI...为了有效地利用蛋白质串联质谱数据,提高蛋白质鉴定的准确性,提出了一种基于信息论的蛋白质数据库搜索鉴定算法——ITPIA(information theory based protein identification algorithm)算法.针对多肽串联质谱质量低、噪音多等问题,ITPIA算法利用了信息论中的熵理论提出了一种有效的实验串联质谱和多肽的理论质谱的匹配打分算法.该算法更大程度上从多肽串联质谱中获得蛋白质的结构信息.实验结果表明,ITPIA算法有效地提高了蛋白质鉴定的准确性.展开更多
In this study, we present a preprocessing method for quadrupole time-of-flight （Q-TOF） tandem mass spectra to increase the accuracy of database searching for peptide （protein） identification. Based on the natural ...In this study, we present a preprocessing method for quadrupole time-of-flight （Q-TOF） tandem mass spectra to increase the accuracy of database searching for peptide （protein） identification. Based on the natural isotopic information inherent in tandem mass spectra, we construct a decision tree after feature selection to classify the noise and ion peaks in tandem spectra. Furthermore, we recognize overlapping peaks to find the monoisotopic masses of ions for the following identification process. The experimental results show that this preprocessing method increases the search speed and the reliability of peptide identification.展开更多
Foraminifera are highly diverse and have a long evolutionary history.As key bioindicators,their phylogenetic schemes are of great importance for paleogeographic applications,but may be hard to recognize correctly.The ...Foraminifera are highly diverse and have a long evolutionary history.As key bioindicators,their phylogenetic schemes are of great importance for paleogeographic applications,but may be hard to recognize correctly.The phylogenetic relationships within the prominent genus Amphistegina are still uncertain.Molecular studies on Amphistegina have so far only focused on genetic diversity within single species and suggested a cryptic diversity that demands for further investigations.Besides molecular sequencing-based approaches,different mass spectrometry-based proteomics approaches are increasingly used to give insights into the relationship between samples and organisms,especially as these do not require reference databases.To better understand the relationship of amphisteginids and test different proteomics-based approaches we applied de novo peptide sequencing and similarity clustering to several populations of Amphistegina lobifera,A.lessonii and A.gibbosa.We also analyzed the dominant photosymbiont community to study their influence on holobiont proteomes.Our analyses indicate that especially de novo peptide sequencing allows to reconstruct the relationship among foraminiferal holobionts,although the detected separation of A.gibbosa from A.lessonii and A.lobifera may be partly influenced by their different photosymbiont types.The resulting dendrograms reflect the separation in two lineages previously suggested and provide a basis for future studies.展开更多
文摘为了有效地利用蛋白质串联质谱数据,提高蛋白质鉴定的准确性,提出了一种基于信息论的蛋白质数据库搜索鉴定算法——ITPIA(information theory based protein identification algorithm)算法.针对多肽串联质谱质量低、噪音多等问题,ITPIA算法利用了信息论中的熵理论提出了一种有效的实验串联质谱和多肽的理论质谱的匹配打分算法.该算法更大程度上从多肽串联质谱中获得蛋白质的结构信息.实验结果表明,ITPIA算法有效地提高了蛋白质鉴定的准确性.
基金supported by the National Basic Research Program(973 Program)of China(No.2002CB713807)the National Key Technologies R&D Program of China(No.2004BA711A21)
文摘In this study, we present a preprocessing method for quadrupole time-of-flight （Q-TOF） tandem mass spectra to increase the accuracy of database searching for peptide （protein） identification. Based on the natural isotopic information inherent in tandem mass spectra, we construct a decision tree after feature selection to classify the noise and ion peaks in tandem spectra. Furthermore, we recognize overlapping peaks to find the monoisotopic masses of ions for the following identification process. The experimental results show that this preprocessing method increases the search speed and the reliability of peptide identification.
基金funded by the Leibniz Association(No.SAW-2014-ISAS-2)awarded to Hildegard Westphal,Albert Sickmann and Jorg Rahnenführer。
文摘Foraminifera are highly diverse and have a long evolutionary history.As key bioindicators,their phylogenetic schemes are of great importance for paleogeographic applications,but may be hard to recognize correctly.The phylogenetic relationships within the prominent genus Amphistegina are still uncertain.Molecular studies on Amphistegina have so far only focused on genetic diversity within single species and suggested a cryptic diversity that demands for further investigations.Besides molecular sequencing-based approaches,different mass spectrometry-based proteomics approaches are increasingly used to give insights into the relationship between samples and organisms,especially as these do not require reference databases.To better understand the relationship of amphisteginids and test different proteomics-based approaches we applied de novo peptide sequencing and similarity clustering to several populations of Amphistegina lobifera,A.lessonii and A.gibbosa.We also analyzed the dominant photosymbiont community to study their influence on holobiont proteomes.Our analyses indicate that especially de novo peptide sequencing allows to reconstruct the relationship among foraminiferal holobionts,although the detected separation of A.gibbosa from A.lessonii and A.lobifera may be partly influenced by their different photosymbiont types.The resulting dendrograms reflect the separation in two lineages previously suggested and provide a basis for future studies.
