{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Geiszler DJ"],"funding":["NCI NIH HHS","National Institutes of Health","NIGMS NIH HHS"],"pagination":["100018"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7950090"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["20"],"pubmed_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"],"journal":["Molecular & cellular proteomics : MCP"],"pubmed_title":["PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results."],"pmcid":["PMC7950090"],"funding_grant_id":["R01 GM094231","R01 GM135504","T32 GM070449","T32 CA140044","U24 CA210967"],"pubmed_authors":["Leprevost FDV","Avtonomov DM","Geiszler DJ","Yu F","Kong AT","Nesvizhskii AI"],"additional_accession":[]},"is_claimable":false,"name":"PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.","description":"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","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021","modification":"2026-05-09T09:50:38.922Z","creation":"2025-04-06T13:14:19.091Z"},"accession":"S-EPMC7950090","cross_references":{"pubmed":["33568339"],"doi":["10.1074/mcp.TIR120.002216"]}}