Electrospray coupled with tandem mass spectrometry is shown to have utility in determining the molecular mass and the sequence of short modified oligonucleotides. The product ion spectrum of a triply deprotonated molecule precursor is dominated by ions formed via two fragmentation pathways: first, fragmentation across the SP-0 phosphate bond, and second, loss of a non-terminal base with concomitant cleavage of the ribose 3'C-O bond. If either of these two pathways is complete with fragmentation occurring at each equivalent position along the phosphadiester backbone, then the oligomer may be sequenced. Alternatively, if both these pathways are only partially complete, their complementarity may be used for more extensive sequencing. The inductive effect of the modification on the nucleobase is shown to influence the latter fragmentation process. The greater the electron affinity of the base modification, the more facile is the loss of that base when the molecule is collisionally activated. In fact, this latter fragmentation dominates the product ion spectrum when a nucleobase contains a substituent that is highly inductively withdrawing. This domination can be such that few other first-generation fragment ions are present in the product ion spectrum. Sequence information may then require utilization of second-generation product ions.

Capillary zone electrophoresis (CZE) coupled with negative ion electrospray mass spectrometry (ES-MS) is used for the detection and identification of adducts formed from the reaction of DNA with (+/-)-anti-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol 9,10-epoxide (BPDE),an active metabolite of benzo[a]pyrene (BaP). Results presented in this paper demonstrate low nanogram detection limits ( < 10 ng or < 15 pmol) for normal scan spectra and collision-induced dissociation spectra of the main nucleotide adduct formed from this reaction. (BPDE reacts predominantly with the exocyclic amino group of guanine.) Exploitation of selective reaction monitoring (SRM) produces detection limits in the low picogram range ( < 85 pg or < 130 fmol). The application of sample stacking significantly increases the concentration detection limit (to approximately 10(-8) M). Nucleotide adducts are negatively charged at most pHs and are therefore ideally suited to the stacking process used in this research. These techniques have been applied to the analysis of the adducts formed from the in vitro reaction of BPDE with DNA. In addition it is shown that CZE-ES-MS, combined with solid-phase sample cleanup, can detect adducts at levels of four adducts in 10(7) unmodified bases or less.

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is shown to give inaccurate results for the analysis of low molecular weight ethoxylate polymers. It is demonstrated that when the degree of ethoxylation is low (n < 9), MALDI-TOFMS produces substantially higher values for the number-average molecular weight (M n ) than obtained with more classical methods such as NMR spectrometry and a wet chemical method to determine the hydroxyl number. Apparently, this is the result of discrimination of the former technique against lower molecular weight ethoxylates in a polymer distribution. The results presented in this paper demonstrate this discrimination through the analysis of a series of ethoxylates with progressively lower M n values. It was also found that by derivatization of the polymer with phthalic anhydride, to produce the carboxylate derivative, the discrimination is reduced and data obtained with MALDI-TOFMS match more precisely the results obtained with the other methods.