The graphical user interface of the software is used to enter the information required to calculate the polymer fragments. These are the polymer class, repeat unit, initiating and terminating end groups, number of repeats, and cation. Both types of chemical structure representation are acceptable such as “CH3CH2” or “C2H5.” The MS/MS data to be annotated are read from an ASCII text file containing mass intensity information (Please note that the mass and intensity values should be separated by a space character) Given a user-selected mass accuracy error (in Daltons), fragments are computed by the software and are matched to experimentally observed peaks. Each matched peak is displayed with a color corresponding to each fragment type and annotated with the fragment information. Matched peaks are also displayed in a table. The user can interact with the table and edit the peak annotation, add annotation to peaks not matched by the software, or delete the annotation from incorrectly assigned peaks.
The ESI-MS/MS spectrum from the lithiated octadecamer (18-mer) of PMMA was imported into the software as a text file and the suggested repeat unit, initiating (alpha), and terminating (omega) end groups were input as empirical formulae (C5H8O2, C5H9O2, and H in the “Main Unit,” “Alpha,” and “Omega” input boxes, respectively). The class of polymer (“Acrylates”) was selected, the cation used to ionize the oligomer (Li in “Cation”), the number of repeat units (17 in “Repeats”), and the mass accuracy (0.2 Da in “Error (Da),” as the data were acquired without the precursor ion, or an external calibrant, used as lock mass were both entered and the “Annotate” button was selected. The resulting annotated spectrum is displayed in Figure 1, along with a table of proposed fragment ions. The latter details the calculated m/z of the fragment matched (“Theoretical Mass”), the fragment annotation (“Description”), the experimental m/z (“Observed Mass”), the difference between theoretical and experimental m/z in Daltons [“Error (Da)”], and the relative intensity of the matched peak (“Intensity”). The color used to highlight each fragment ion is also shown in the “Highlight Color” column of this table, with a series of peaks (e.g., from the A series in Figure 1) displayed in the same color. The annotation and highlighting of each peak can be temporarily removed using the “Display” column of the table (clicking on the checkbox in that column for the relevant peak) or custom annotation and/or coloring can be added as required. This means that peaks originating from a novel fragmentation pathway, for example, can be annotated if required. This could be useful when annotating MS/MS spectra of PMMA that contain halogenated end groups, which have been shown to contain some peaks originating from loss of parts of this end group and the polymer backbone, in addition to the expected fragmentation for this methacrylate. The data from this table can be exported from the software, as a comma separated value (.csv) file to be used in other applications.
Thalassinos, K., Jackson, A. T., Williams, J. P., Hilton, G. R., Slade, S. E. and Scrivens, J. H. (2007). Novel software for the assignment of peaks from tandem mass spectrometry spectra of synthetic polymers. Journal of the American Society for Mass Spectrometry 18:1324-1331.