Tandem mass spectrometry sequencing in the negative ion mode to read binary information encoded in sequence‐defined poly(alkoxyamine amide)s

Rationale Digitally encoded oligomers composed of two distinct amide coding units spaced by a nitroxide moiety were recently decrypted using a tandem mass spectrometry (MS/MS) sequencing approach developed for protonated oligomers. Here, the MS/MS behavior of deprotonated oligomers was explored in the negative ion mode to provide both structural and mechanistic complementary information. Methods Binary‐encoded oligo(alkoxyamine)amides, containing coding 0 / 1 amide units spaced by a TEMPO nitroxide moiety, were ionized in negative ion mode electrospray thanks to their α end‐group containing a carboxylic acid function. Deprotonated molecules were subjected to collision‐induced dissociation in MS/MS and MS 3 experiments, combined with accurate mass measurements, for a thorough investigation of their dissociation behavior. Results Deprotonated oligomers readily dissociated upon collisional activation via competitive homolytic cleavages of all fragile alkoxyamine linkages between any coding 0 or 1 monomers and a nitroxide moiety. As expected, only product ions holding the deprotonated α end‐group were detected while complementary moieties containing the ω termination were released as radicals. The so‐formed distonic radical anions were observed to further depolymerize according to a radical‐induced process, as evidenced by MS 3 experiments. Conclusions Messages encoded in oligo(alkoxyamine)amides were readily decrypted by MS/MS sequencing performed in the negative ion mode. When compared with results obtained in positive ion mode ESI‐MS/MS, these data provided further evidence regarding the influence of adducted proton on the charge‐remote homolytic cleavage of alkoxyamine linkages. Copyright © 2015 John Wiley & Sons, Ltd.