Protein mass spectrometry imaging (MSI) with electrospray-based
ambient ionization techniques, such as nanospray desorption electrospray
ionization (nano-DESI), generates data sets in which each pixel corresponds
to a mass spectrum populated by peaks corresponding to multiply charged
protein ions. Importantly, the signal associated with each protein
is split among multiple charge states. These peaks can be transformed
into the mass domain by spectral deconvolution. When proteins are
imaged under native/non-denaturing conditions to retain non-covalent
interactions, deconvolution is particularly valuable in helping interpret
the data. To improve the acquisition speed, signal-to-noise ratio,
and sensitivity, native MSI is usually performed using mass resolving
powers that do not provide isotopic resolution, and conventional algorithms
for deconvolution of lower-resolution data are not suitable for these
large data sets. UniDec was originally developed to enable rapid deconvolution
of complex protein mass spectra. Here, we developed an updated feature
set harnessing the high-throughput module, MetaUniDec, to deconvolve
each pixel of native MSI data sets and transform m/z-domain image files to the mass domain. New tools
enable the reading, processing, and output of open format .imzML files
for downstream analysis. Transformation of data into the mass domain
also provides greater accessibility, with mass information readily
interpretable by users of established protein biology tools such as
sodium dodecyl sulfate polyacrylamide gel electrophoresis.