Convenient Graphical Visualization of Messages Encoded in Sequence‐Defined Synthetic Polymers Using Kendrick Mass Defect Analysis of their MS/MS Data

Abstract

Kendrick mass defect (KMD) analysis is shown here to be a convenient method to read binary messages encoded in the structure of two types of sequence‐defined synthetic polymers, namely, polyurethanes and poly(alkoxyamine phosphodiester)s. KMD analysis allows graphical ranking of mass data obtained for species containing repeating units. This is performed on MS/MS data in which distribution of fragments reveals the comonomer sequence of digital macromolecules. Choosing one coding monomer as the base unit, KMD computation of MS/MS data leads to stair‐like plots where flat steps correspond to that monomer selected as the base unit while oblique steps reveal the other monomer. To correct for any point misalignments resulting from slight inaccuracy of fragment mass measurement, fractional base units are used to perform resolution‐enhanced KMD (RE‐KMD) analysis. As the length of the chain increased, a procedure aiming at correct aliased points is also implemented to achieve continuous, more convenient, stair‐like plots.

Analysis of monodisperse, sequence-defined, and POSS-functionalized polyester copolymers by MALDI tandem mass spectrometry

“…Kendrick mass defect (KMD) analysis has been used as a convenient tool to visualize the binary code embedded in sequence-defined polymers. 29 Such data treatment typically presupposes that MS 2 spectra measured at high mass resolution and high mass accuracy are available. In this study, a remainder of Kendrick mass (RKM) analysis was employed due to the lower mass accuracies encountered upon MALDI-MS 2 of ions with high m/z ratio.…”

Real divisors and pseudo‐continuous enhancement of resolution for a Kendrick mass defect analysis

“…Homologous ions form a polymeric distribution and thus line up horizontally in a KMD plot displaying KMDs versus m / z while different distributions are displayed as parallel lines . This is an elegant data processing and visualization tool used to filter background peaks in congested mass spectra, or instantly sort polymer ion series by their repeat units, end‐groups, adducted ions and charge states among other features . A regular KMD analysis depends on R only and produces a single plot often displaying clustered clouds of points along a limited part of the y ‐axis.…”

“…The resolution‐enhanced KMD plot is thus a dynamic graph suitable for mass measurements of ultrahigh to medium accuracy . Positive natural divisors X ∈ ℤ + within a “recommended range” have been proposed earlier for ease of practical use . However, the use of positive real numbers has been suggested to increase the number of divisors denoted x ∈ ℝ + and hypothetically achieve a “continuous” enhancement of resolution as discussed hereafter.…”

Promoting carboxylate salts in the ESI source to simplify positive mode MS/MS sequencing of acid-terminated encoded polyurethanes

“…As a result, coded sequences could be literally read from peak-to-peak distance in MS/MS spectra and a simple algorithm was created for automated extraction of digital data [15]. Alternatively, the code could be graphically read using Kendrick mass defect plots [16]. Although optimal for straightforward MS/MS decoding in the negative ion mode, sequence-defined PUs exhibited decreasing ionization yield as their chain length increased.…”