PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.

ABSTRACT: Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of post-translational modification profiles detected in open searches based on attributes, such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multiexperiment comparisons for studying changes in modification profiles, e.g., in data generated in different labo

SUBMITTER: Geiszler DJ 

PROVIDER: S-EPMC7950090 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature