Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics

Recent studies have revealed diverse
amino acid, post-translational,
and noncanonical modifications of proteins in diverse organisms and
tissues. However, their unbiased detection and analysis remain hindered
by technical limitations. Here, we present a spectral alignment method
for the identification of protein modifications using high-resolution
mass spectrometry proteomics. Termed SAMPEI for spectral alignment-based
modified peptide identification, this open-source algorithm is designed
for the discovery of functional protein and peptide signaling modifications,
without prior knowledge of their identities. Using synthetic standards
and controlled chemical labeling experiments, we demonstrate its high
specificity and sensitivity for the discovery of substoichiometric
protein modifications in complex cellular extracts. SAMPEI mapping
of mouse macrophage differentiation revealed diverse post-translational
protein modifications, including distinct forms of cysteine itaconatylation.
SAMPEI’s robust parametrization and versatility are expected
to facilitate the discovery of biological modifications of diverse
macromolecules. SAMPEI is implemented as a Python package and is available
open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).