# Switching Ionization Polarity to Simplify MS/MS Sequencing of Digital Polymers: the Case of Informational Poly(Amino phosphodiester)s

## TL;DR

This paper shows how switching ionization polarity in mass spectrometry can simplify reading messages encoded in a special type of polymer.

## Contribution

The study introduces a new method using ionization polarity switching to improve MS/MS sequencing of informational polymers.

## Key findings

- Protonated N-PPDEs produce simpler and more reliable MS/MS patterns compared to deprotonated species.
- Switching to positive ion mode preserves phosphate linkages and reduces signal complexity.
- This approach enables more accurate sequencing of long informational polymers.

## Abstract

MS/MS sequencing is commonly used to read binary messages encoded in digital polymers. To achieve full sequence coverage required for error‐free reading, the structure of coding units is usually optimized to prevent extensive signal dilution over multiple fragmentation routes. Changing ionization polarity can also have a significant effect on MS/MS pattern, which is explored here for poly(amino phosphodiester)s.

Poly(amino phosphodiester)s (N‐PPDEs) include comonomers composed of one phosphate group and a main‐chain tertiary amine holding different alkyl substituents as coding moieties. Accordingly, they can be readily ionized in both polarity modes, using ammonium acetate to promote electrospray formation of deprotonated species and protonated molecules when switching from negative to positive ion mode. Changes of their MS/MS spectra are studied with regard to the behavior of their PPDE homologues lacking the main‐chain tertiary amine.

In collision‐induced dissociation (CID) conditions, eight fragment series are produced upon cleavage of all phosphate bonds in deprotonated species, whereas only four ion series are generated from protonated N‐PPDEs in which O–P–O linkages remain intact. The advantageous MS/MS behavior of protonated N‐PPDEs has been rationalized by considering that protons located on tertiary amines are also solvated by nearby phosphate groups, promoting exclusive cleavage of C–O bonds.

In contrast to PPDEs, switching from deprotonated to protonated precursors yields highly simplified CID data for N‐PPDEs, opening promising perspectives for reliable MS/MS sequencing of long coded polymers.