title: GenoMass--a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests.
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.
authors.affiliation: Mass Spectrometry Center, FAS Center for System Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Liao
authors.forename: Chang
authors.initials: C
authors.lastname: Shen
authors.forename: Paul
authors.initials: P
authors.lastname: Vouros
mesh_terms: D015073:2-Acetylaminofluorene / Q000378:metabolism; D000099:Acetoxyacetylaminofluorene / Q000378:metabolism; D000469:Alkaline Phosphatase / Q000378:metabolism; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D004247:DNA / Q000032:analysis* / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000378:metabolism; D004722:Endoribonucleases / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000032:analysis* / Q000378:metabolism; D012984:Software
chemical_list: D009841:Oligonucleotides; D000099:Acetoxyacetylaminofluorene; D004247:DNA; D015073:2-Acetylaminofluorene; D004706:Endodeoxyribonucleases; D004722:Endoribonucleases; D000469:Alkaline Phosphatase; C021835:Serratia marcescens nuclease