Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32415162", "kind": "science-record", "revision": 4, "content_hash": "sha256:7a2bbe2f674c261b85e6a92e3f19116251a0ea99e88b5722359618bfb71a6495", "created_at": "2026-11-01T15:41:01Z", "updated_at": "2026-11-01T21:23:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes.", "doi": "10.1038/s41597-020-0487-6", "pmid": "32415162", "authors": ["Gerd Specht", "Hanna P Roetschke", "Artem Mansurkhodzhaev", "Petra Henklein", "Kathrin Textoris-Taube", "Henning Urlaub", "Michele Mishto", "Juliane Liepe"], "journal": "Scientific data", "year": 2020, "abstract": "Proteasomes are the main producers of antigenic peptides presented to CD8+ T cells. They can cut proteins and release their fragments or recombine non-contiguous fragments thereby generating novel sequences, i.e. spliced peptides. Understanding which are the driving forces and the sequence preferences of both reactions can streamline target discovery in immunotherapies against cancer, infection and autoimmunity. Here, we present a large database of spliced and non-spliced peptides generated by proteasomes in vitro, which is available as simple CSV file and as a MySQL database. To generate the database, we performed in vitro digestions of 55 unique synthetic polypeptide substrates with different proteasome isoforms and experimental conditions. We measured the samples using three mass spectrometers, filtered and validated putative peptides, identified 22,333 peptide product sequences (15,028 spliced and 7,305 non-spliced product sequences). Our database and datasets have been deposited to the Mendeley (doi:10.17632/nr7cs764rc.1) and PRIDE (PXD016782) repositories. We anticipate that this unique database can be a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing, with various future translational applications.", "claims": [{"id": "claim-method", "statement": "Differences in distributions have been tested using the Kolmogorov-Smirnov test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32415162", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Differences in distributions have been tested using the Kolmogorov-Smirnov test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The algorithm generating all possible cis and trans spliced peptides was originally described by Liepe et al.56. 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"section_title": "Database", "row_count": 24, "column_count": 2}, "table": {"label": "Table 1", "caption": "Database description.", "rows": [["Column name", "Description"], ["sampleID", "Unique identifier for every sample"], ["sampleName", "Sample Name used during experiment"], ["runID", "Technical replicate number"], ["protIsotype", "proteasome isoform used for digestion"], ["digestTime", "Elapsed digestion time (hours) at time of measurement"], ["species", "species origin for used proteasome"], ["sampleDate", "Sample date"], ["instrument", "Instrument used for measurement"], ["fragmentation", "Fragmentation method used for measurement"], ["substrateOrigin", "Biological origin of substrate"], ["location", "Measurement location"], ["substrateSeq", "Amino acid sequence of substrate"], ["substrateID", "Unique identifier for a substrate sequence"], ["pepSeq", "Amino acid sequence of peptide products"], ["scanNum", "Scan Number listed in the RAW file"], ["rankMS", "Peptide rank assigned by Mascot Server"], ["ionScore", "Ion Score assigned by Mascot Server"], ["qValue", "Q-Value assigned by Mascot Server"], ["productType", "PCP: non-spliced peptide; PSP: spliced peptide"], ["spliceType", "PSP: cis, reverse cis or trans spliced peptides"], ["positions", "Peptide sequence described as amino acid positions in the substrate sequence"], ["charge", "Ion charge"], ["PTM", "Post-translational modifications"]], "row_count": 24, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32415162:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34ec29fc77820ca060dddb1fa9066ee9ea213961f845c92a4c887033ec61ea0a", "bytes": 3111, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Tests for statistical differences between characteristics of identified peptides.", "structure": {"pmcid": "PMC7228940", "section_index": 12, "section_title": "Spliced and non-spliced peptide analysis and further validations", "row_count": 41, "column_count": 3}, "table": {"label": "Table 2", "caption": "Tests for statistical differences between characteristics of identified peptides.", "rows": [["Group 1", "Group2", "p-value"], ["Peptide length"], ["Non-spliced products", "Non-spliced synthesis artifacts", "<2e-16"], ["Non-spliced products", "Non-spliced random control", "<2e-16"], ["Non-spliced synthesis artifacts", "Non-spliced random control", "<2e-16"], ["cis spliced products", "cis spliced synthesis artifacts", "<2e-16"], ["cis spliced products", "cis spliced random control", "<2e-16"], ["cis spliced synthesis artifacts", "cis spliced random control", "<2e-16"], ["trans spliced products", "trans spliced synthesis artifacts", "<2e-16"], ["trans spliced products", "trans spliced random control", "<2e-16"], ["trans spliced 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