5/24/2023 0 Comments Basic protein sequence analysisAs a result, only a subset of peptides present in the sample will be identified. Identification coverage problem: Because of the complexity of proteomics data and the limitations of existing peptide identification algorithms, most tandem mass spectra in a typical proteomics experiment cannot be recognized confidently. This is because several technical challenges remain unsolved : the identification coverage problem, the identification ambiguity problem, and the identification validation problem. However, such protein inference problem is still far from being resolved. Because proteins are more biologically relevant than peptides, it is critical to accurately infer all proteins present in the sample from identified peptides. Protein identification is one of most important problems in shotgun proteomics. Zengyou He, in Data Mining for Bioinformatics Applications, 2015 5.7 Discussion and future perspective Another important point for successful protein identification by PMF is correct enzyme specificity. It is shown that mass accuracy of 50 ppm gives a good result for protein identification by PMF. The success of identifying a correct protein depends on the accuracy of the mass of the peptides that is used for comparison. MALDI-ToF is commonly used mass spectrometry for protein identification by PMF, a rapid and sensitive technique for protein molecular mass determination. Mass spectrometry replaced the cumbersome protein chemistry-based protein identification. They became a handy tool for peptide mass determination. These techniques are sensitive, work with the femtomole quantity of the sample and the mass range is up to 200 kDa. MALDI and ESI mass spectrometric techniques were introduced in 1992. Due to the lack of sensitivity of FAB, mass spectrometric data was not utilized for other studies. The lysozyme was successfully identified by correlating the measured peptide mass with the already existing peptide mass of lysozyme by using a computer program called FRAGFIT. Application of mass spectrometric data for protein identification was tested using the fast atom bombardment ( FAB) mass spectrum of trypsin digested lysozyme. A faster method of protein identification was needed to cope with genome sequencing projects. Protein identification is done after sequencing by Edman degradation but this is a time-consuming method and also limited by the size of the protein sequence that can be determined. The ultimate way of describing any protein is by its sequence as that is unique to a particular protein. Although proteins are separated by 2D-PAGE which reveals some parameters about the proteins such as pI and molecular weight, theses two criteria are not sufficient to describe a protein completely. Protein identification is an important step in the characterization of a protein for further studies. Nachimuthu Saraswathy, Ponnusamy Ramalingam, in Concepts and Techniques in Genomics and Proteomics, 2011 13.1 Introduction
0 Comments
Leave a Reply. |