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Author Ning, K.; Chong, K.F.; Leong, H.W.
Title A database search algorithm for identification of peptides with multiple charges using tandem mass spectrometry Type Book Chapter
Year 2006 Publication Data Mining for Biomedical Applications, Proceedings Abbreviated Journal
Volume Issue Pages 2-13
Keywords protein identification; sequence databases
Abstract Peptide sequencing using tandem mass spectrometry is the process of interpreting the peptide sequence from a given mass spectrum. Peptide sequencing is an important but challenging problem in bioinformatics. The advancement in mass spectrometry machines has yielded great amount of high quality spectra data, but the methods to analyze these spectra to get peptide sequences are still accurate. There are two types of peptide sequencing methods -database search methods and the de novo methods. Much progress has been made, but the accuracy and efficiency of these methods are not satisfactory and improvements are urgently needed. In this paper, we will introduce a database search algorithm for sequencing of peptides using tandem mass spectrometry. This Peptide Sequence Pattern (PSP) algorithm first generates the peptide sequence patterns (PSPs) by connecting the strong tags with mass differences. Then a linear time database search process is used to search for candidate peptide sequences by PSPs, and the candidate peptide sequences are then scored by share peaks count. The PSP algorithm is designed for peptide sequencing from spectra with multiple charges, but it is also applicable for singly charged spectra. Experiments have shown that our algorithm can obtain better sequencing results than current database search algorithms for many multiply charged spectra, and comparative results for singly charged spectra against other algorithms.
Address
Corporate Author Thesis
Publisher Springer-Verlag Berlin Place of Publication Berlin Editor Li, J.; Yang, Q.; Tan, A.H.
Language Summary Language Original Title
Series Editor Series Title Lecture Notes in Computer Science Abbreviated Series Title
Series Volume (down) 3916 Series Issue Edition
ISSN ISBN Medium
Area Expedition Conference
Notes ISI Document Delivery No.: BEG77 Times Cited: 1 Cited Reference Count: 15 Cited References: CHONG KF, 2006, IN PRESS APBC2006 CRAIG R, 2004, J PROTEOME RES, V3, P1234, DOI 10.1021/pr049882h DANCIK V, 1999, J COMPUT BIOL, V6, P327 ENG JK, 1994, J AM SOC MASS SPECTR, V5, P976 FENYO D, 1998, ELECTROPHORESIS, V19, P998 FRANK A, 2005, ANAL CHEM, V77, P964, DOI 10.1021/ac048788h GUSTFIELD D, 1997, ALGORITHM STRINGS TR HAN Y, 2004, 2004 IEEE COMP SYST KELLER A, 2002, OMICS, V6, P207 MA B, 2003, RAPID COMMUN MASS SP, V17, P2337, DOI 10.1002/rcm.1196 MANN M, 1994, ANAL CHEM, V66, P4390 PERKINS DN, 1999, ELECTROPHORESIS, V20, P3551 PEVZNER P, 2000, INT C COMP MOL BIOL, P231 TANNER S, 2005, UNPUB INSPECT FAST A WU S, 1992, P USENIX WINT 1992 T, P153 Proceedings Paper 1stWorkshop on Data Mining for Biomedical Applications Apr 09, 2006 Singapore, SINGAPORE Nanyang Technol Univ, Sch Comp Engn, Inst Infocomm Res Heidelberger platz 3, d-14197 berlin, germany Approved no
Call Number refbase @ admin @ Ning2006 Serial 24673
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Author Claveirole, T.; Lombardy, S.; OConnor, S.; Pouchet, L.-N.; Sakarovitch, J.
Title Inside Vaucanson Type Book Chapter
Year 2006 Publication Implementation and Application of Automata Abbreviated Journal
Volume Issue Pages 116-128
Keywords
Abstract
Address
Corporate Author Thesis
Publisher Springer-Verlag Place of Publication Editor Farré, J.; Litovsky, I.; Schmitz, S.
Language Summary Language Original Title
Series Editor Series Title Lecture Notes in Computer Science Abbreviated Series Title
Series Volume (down) 3845 Series Issue Edition
ISSN ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number refbase @ user @ claveirole06ic Serial 740
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Author de la Higuera, C.; Piat, F.; Frédéric, T.
Title Learning Stochastic Finite Automata for Musical Style Recognition Type Book Chapter
Year 2006 Publication Implementation and Application of Automata Abbreviated Journal
Volume Issue Pages 345-346
Keywords
Abstract
Address
Corporate Author Thesis
Publisher Springer-Verlag Place of Publication Editor Farré, J.; Litovsky, I.; Schmitz, S.
Language Summary Language Original Title
Series Editor Series Title Lecture Notes in Computer Science Abbreviated Series Title
Series Volume (down) 3845 Series Issue Edition
ISSN ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number refbase @ user @ delahiguera06ic Serial 871
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Author Tao, J.; Tan, T.
Title Affective Computing: A Review Type Book Chapter
Year 2005 Publication Affective Computing and Intelligent Interaction Abbreviated Journal
Volume Issue Pages 981-995
Keywords
Abstract
Address
Corporate Author Thesis
Publisher Springer-Verlag Place of Publication Editor Tao, J.; Tan, T.; Picard, R.
Language Summary Language Original Title
Series Editor Series Title Lecture Notes in Computer Science Abbreviated Series Title
Series Volume (down) 3784 Series Issue Edition
ISSN ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number refbase @ user @ tao05ic Serial 1149
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Author Ma, C.; Prendinger, H.; Ishizuka, M.
Title A Chat System Based on Emotion Estimation from Text and Embodied Conversational Messengers Type Book Chapter
Year 2005 Publication Entertainment Computing – ICEC 2005 Abbreviated Journal
Volume Issue Pages 535-538
Keywords
Abstract
Address
Corporate Author Thesis
Publisher Springer-Verlag Place of Publication Editor Kishino, F.; Kitamura, Y.; Kato, H.; Nagata, N.
Language Summary Language Original Title
Series Editor Series Title Lecture Notes in Computer Science Abbreviated Series Title
Series Volume (down) 3711 Series Issue Edition
ISSN ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number refbase @ user @ ma05ic Serial 960
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