You Li, Hao Chi, Leihao Xia, Xiaowen Chu
BACKGROUND: Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines […]
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You Li, Xiaowen Chu
Database searching is a main method for protein identification in shotgun proteomics, and many research efforts are dedicated to improving its effectiveness. However, the efficiency of database searching is facing a serious challenge, due to the ever fast growth of protein and peptide databases resulted from genome translations, enzymatic digestions, and post-translational modifications (PTMs). On […]
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Heitor Silverio Lopes, Leonardo Magalhaes Cruz
Nowadays it is difficult to imagine an area of knowledge that can continue developing without the use of computers and informatics. It is not different with biology, that has seen an unpredictable growth in recent decades, with the rise of a new discipline, bioinformatics, bringing together molecular biology, biotechnology and information technology. More recently, the […]
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Jian Zhang, I. McQuillan, FangXiang Wu
Tandem mass spectrometry is a powerful experimental tool used in molecular biology to determine the composition of protein mixtures. In a tandem mass experiment, peptide ion selection algorithms generally select only the most abundant peptide ions for further fragmentation. Because of this, the low-abundance proteins in a sample rarely get identified. A Real-Time Peptide-Spectrum Matching […]
Lydia A. Baumgardner, Avinash K. Shanmugam, Henry Lam, Jimmy K. Eng, Daniel B. Martin
Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and […]
J. de Corral, H. Pfister
We present a system for three-dimensional visualization of complex liquid chromatography-mass spectrometry (LCMS) data. Every LCMS data point has three attributes: time, mass, and intensity. Instead of the traditional visualization of two-dimensional subsets of the data, we visualize it as a height field or terrain in 3D. Unlike traditional terrains, LCMS data has non-linear sampling […]

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