A Combined Gas-Phase Separation Strategy for ADP-ribosylated Peptides.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37589412", "kind": "science-record", "revision": 3, "content_hash": "sha256:a01a58d1946b821d32ad7b70c533d830a355eef1bcf0db1e68c25b885c01b6d7", "created_at": "2026-11-01T19:02:23Z", "updated_at": "2026-11-01T22:10:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Combined Gas-Phase Separation Strategy for ADP-ribosylated Peptides.", "doi": "10.1021/jasms.3c00129", "pmid": "37589412", "authors": ["Taku Kasai", "Shiori Kuraoka", "Hideyuki Higashi", "Bernard Delanghe", "Masanori Aikawa", "Sasha A Singh"], "journal": "Journal of the American Society for Mass Spectrometry", "year": 2023, "abstract": "ADP-ribosylation (ADPr) is a post-translational modification that is best studied using mass spectrometry. Method developments that are permissive with low inputs or baseline levels of protein ribosylation represent the next frontier in the field. High-field asymmetric waveform ion mobility spectrometry (FAIMS) reduces peptide complexity in the gas phase, providing a means to achieve maximal ADPr peptide sequencing depth. We therefore investigated the extent to which FAIMS with or without traditional gas-phase fractionation-separation (GPS) can increase the number of ADPr peptides. We examined ADPr peptides enriched from mouse spleens. We gleaned additional insight by also reporting findings from the corresponding non-ADPr peptide contaminants and the peptide inputs for ADPr peptide enrichment. At increasingly higher negative compensation voltages, ADPr peptides were more stable, whereas the non-ADPr peptides were filtered out. A combination of 3 GPS survey scans, each with 8 compensation voltages, resulted in 790 high-confidence ADPr peptides, compared to 90 with GPS alone. A simplified acquisition strategy requiring only two injections corresponding to two MS1 scan ranges coupled to optimized compensation voltage settings provided 402 ADPr peptides corresponding to 234 ADPr proteins. We conclude that our combined GPS strategy is a valuable addition to any ADP-ribosylome workflow. The data are available via ProteomeXchange with identifier PXD040898.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE33 partner repository with the data set identifiers PXD040898 and 10.6019/PXD040898.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37589412", "locator": "sections[14] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE33 partner repository with the data set identifiers PXD040898 and 10.6019/PXD040898."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Combining gas-phase fractionation–separation with seven FAIMS compensation voltages across three survey-scan ranges increased mouse-spleen-derived high-confidence ADPr peptide identifications from 90 with GPS alone to 790.", "kind": "quantitative", "target": {"value": 8.8, "unit": "fold change", "tolerance": null, "source": "We increased the number of mouse-spleen-derived high-confidence ADPr peptides 8.8-fold when combining seven CVs within three GPS MS1 scans (790 ADPr peptides) versus GPS alone (90 ADPr peptides)."}, "evidence": [{"asset": "source:pmid:37589412", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A combination of 3 GPS survey scans, each with 8 compensation voltages, resulted in 790 high-confidence ADPr peptides, compared to 90 with GPS alone."}, {"asset": "source:pmid:37589412", "locator": "sections[13] \"Conclusions\" paragraph 2", "quote": "We increased the number of mouse-spleen-derived high-confidence ADPr peptides 8.8-fold when combining seven CVs within three GPS MS1 scans (790 ADPr peptides) versus GPS alone (90 ADPr peptides)."}, {"asset": "source:pmid:37589412", "locator": "sections[12] \"Simplified GPS + FAIMS Acquisition Strategy\" paragraph 2", "quote": "When compared to the number of ADPr peptides and proteins acquired with 18 injections, the simplified acquisition strategy recovered 345 of 790 ADPr peptides, while providing 57 unique ADPr peptides, and 200 of 383 ADPr proteins, providing 34 unique ADPr proteins."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Combining gas-phase fractionation–separation with seven FAIMS compensation voltages across three survey-scan ranges increased mouse-spleen-derived high-confidence ADPr peptide identifications from 90 with GPS alone to 790.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37589412"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Method developments that are permissive wit", "r peptide enrichment itself (Figure 1A). The mass spectrometric properties of both “input peptides” and “non", "e more useful to compare/contrast the unique mass spectrometric properties of their ADPr peptide counterpart", "the spleen (ADPr) peptides (Figure 1A) (see LC-MS/MS in the Experimental Section). Supplementary"], "order_basis": "paper_text_order:114", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["des. We examined ADPr peptides enriched from mouse spleens. 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