Enhanced Global Post-translational Modification Discovery with MetaMorpheus

Correct identification of protein
post-translational modifications
(PTMs) is crucial to understanding many aspects of protein function
in biological processes. G-PTM-D is a recently developed technique
for global identification and localization of PTMs. Spectral file
calibration prior to applying G-PTM-D, and algorithmic enhancements
in the peptide database search significantly increase the accuracy,
speed, and scope of PTM identification. We enhance G-PTM-D by using
multinotch searches and demonstrate its effectiveness in identification
of numerous types of PTMs including high-mass modifications such as
glycosylations. The changes described in this work lead to a 20% increase
in the number of identified modifications and an order of magnitude
decrease in search time. The complete workflow is implemented in MetaMorpheus,
a software tool that integrates the database search procedure, identification
of coisolated peptides, spectral calibration, and the enhanced G-PTM-D
workflow. Multinotch searches are also shown to be useful in contexts
other than G-PTM-D by producing superior results when used instead
of standard narrow-window and open database searches.