Comparison of MS/MS methods for characterization of DNA/cisplatin adducts

Abstract

The development of activation/dissociation techniques such as ultraviolet photodissociation (UVPD), infrared multiphoton dissociation (IRMPD), and electron transfer dissociation (ETD) as alternatives to collision induced dissociation (CID) has extended the range of strategies for characterizing biologically relevant molecules. Here, we describe a comprehensive comparison of CID, IRMPD, UVPD, ETD, and hybrid processes termed ETcaD and ET-IRMPD (and analogous hybrid methods in the negative mode NETcaD and NET-IRMPD) for generating sequence-specific fragment ions and allowing adduction sites to be pinpointed for DNA/cisplatin adducts. Among the six MS/MS methods, the numerous products generated by the IRMPD and UVPD techniques resulted in the most specific and extensive backbone cleavages. We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra.

Figure 1

Relative distributions of all ion types upon CID, IRMPD, UVPD, ETD, ETcaD, ETIRMPD for (a) the 3- (or 3-•) charge state and (b) 3+ (or 3+•) charge state of unmodified ss1. The relative portion of each category of ion is obtained by dividing the summed abundance for all fragments in a particular category by the total abundance of all fragment ions.

Figure 2

MS/MS spectra of ss1/cisplatin adduct by (a) CID (3-), (b) IRMPD (3-), (c) 193-nm UVPD (3-), (d) neg ETD (3-), (e) neg ETcaD (3-•), and (f) neg ET-IRMPD (3-•). Precursor ions are noted with a star. Bolded, italicized product ions retain the modification.

Figure 2

MS/MS spectra of ss1/cisplatin adduct by (a) CID (3-), (b) IRMPD (3-), (c) 193-nm UVPD (3-), (d) neg ETD (3-), (e) neg ETcaD (3-•), and (f) neg ET-IRMPD (3-•). Precursor ions are noted with a star. Bolded, italicized product ions retain the modification.

Figure 3

Relative distributions of all ion types upon CID, IRMPD, UVPD, ETD, ETcaD, ETIRMPD for (a) the 3- (or 3-•) charge state and (b) 3+ (or 3+•) charge state of platinated ss1. The relative portion of each category of ion is obtained by dividing the summed abundance for all fragments in a particular category by the total abundance of all fragment ions.

Figure 4

(a) Chromatographic profile elution of two ss5/cisplatin adducts; (b) LCMS/MS spectra for products at 34.5 min and 37.1 min. Precursor ions are noted with a star. Bolded, italicized product ions retain the modification. The fragments in red are important for pinpointing the site of the Pt modification. The fragments in green cannot be assigned confidently due to m/z values that fit several isomeric sequences.