PNNL

Abstract

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify biomolecular isotope profiles from samples like bacterial colonies and tissues. Often MALDI-MS data does not include tandem MS fragmentation data, and thus the identifications of detected signals require external databases for matching to the accurate mass of species in the samples. Most relevant software tools are focused on small molecules (e.g., metabolites, lipids), and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI data for multiple MS omics datatypes (e.g., intact proteomics, lipidomics, etc.). This tool either accepts already computed molecular formulas, or computes molecular formula from a list of input peptides or proteins with support for post-translational modifications from several tools (e.g. TopPIC, pTop, MSPathFinder). Visualization of all matched isotopic profiles are provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort matches scores, number of peaks matched, etc. IsoMatchMS greatly reduces the time to visualize isotope profiles to annotate true biomolecules and for downstream analyses.