Premium
GenoMass ‐ a computer software for automated identification of oligonucleotide DNA adducts from LC‐MS analysis of DNA digests
Author(s) -
Liao Qing,
Shen Chang,
Vouros Paul
Publication year - 2009
Publication title -
journal of mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 121
eISSN - 1096-9888
pISSN - 1076-5174
DOI - 10.1002/jms.1532
Subject(s) - oligonucleotide , chemistry , dna , in silico , adduct , nuclease , nucleobase , computational biology , identification (biology) , software , combinatorial chemistry , biochemistry , computer science , gene , programming language , biology , organic chemistry , botany
Abstract In the investigation of oligonucleotides, DNA and their adducts by LC‐MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a ‘reversed pseudo‐combinatorial’ approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC‐MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites. Copyright © 2008 John Wiley & Sons, Ltd.