biostudies-literatureGeiszler DJNCI NIH HHSNational Institutes of HealthNIGMS NIH HHS100018https://www.ebi.ac.uk/biostudies/studies/S-EPMC7950090biostudies-literatureUnknown20Open 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 laboMolecular & cellular proteomics : MCPPTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.PMC7950090R01 GM094231R01 GM135504T32 GM070449T32 CA140044U24 CA210967Leprevost FDVAvtonomov DMGeiszler DJYu FKong ATNesvizhskii AIfalsePTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.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 labo2021-01-01T00:00:00Z20212026-05-09T09:50:38.922Z2025-04-06T13:14:19.091ZS-EPMC79500903356833910.1074/mcp.TIR120.002216