De Novo Sequencing Using MS/MS Data From Ion Trap

In recent years, mass spectrometry (MS) has been one of the most successful techniques in proteomics research. Especially, the tandem mass spectrometry (MS/MS) has been widely used for high-throughout protein identification. Mass spectrometry can produce a large amount of data, the Data include abundant information of protein structure, but this information need proceed to get the identification result of peptide and protein."Researching of de novo sequencing using tandem mass spectrometry"comes from the building of Protein Expression analyzing system of Human Liver Proteome Project (HLPP).In chapter 1 ,the article introduces background,significance of the researching and the recent status of de novo sequencing. In the last, the article expatiates some thoughts of the tendency of de novo sequencing. Mass spectrometry is a complex system, including of some part. Different part has many choices, so different system has different peculiarity and this is important for the design of mass data processing and de novo sequencing. Mass data has a lot of noise, this will increase the time of peptide identification and low down the accuracy of identification. The processing of mass data is a problem can not be ignored. In chapter 3, the article introduces some methods and combines them. These methods are useful for advancing the speed and accuracy of de novo sequencing. Nine steps method of mass interpretation is base of de novo sequencing. In chapter 4, the article introduces the basic theory of this kind of method and gives some example. Finally, the article introduces a new program basing on nine steps method of mass interpretation. This program can be an aid tool and has been used in the project. The chapter 5 discusses PepNovo,tests and evaluates the program using standard mass data. The results show that the accuracy is good, but because PepNovo justs give the final result, so it can not identify the protein modification and do not fit the need of the project.