DecoID improves identification rates in metabolomics through database-assisted MS/MS deconvolution.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34239103", "kind": "science-record", "revision": 4, "content_hash": "sha256:78133b78af0e01648484a4922a23c314456eeb027ff6bca5d640463b4ed552c5", "created_at": "2026-11-01T17:35:37Z", "updated_at": "2026-11-01T22:04:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DecoID improves identification rates in metabolomics through database-assisted MS/MS deconvolution.", "doi": "10.1038/s41592-021-01195-3", "pmid": "34239103", "authors": ["Ethan Stancliffe", "Michaela Schwaiger-Haber", "Miriam Sindelar", "Gary J Patti"], "journal": "Nature methods", "year": 2021, "abstract": "Chimeric MS/MS spectra contain fragments from multiple precursor ions and therefore hinder compound identification in metabolomics. Historically, deconvolution of these chimeric spectra has been challenging and relied on specific experimental methods that introduce variation in the ratios of precursor ions between multiple tandem mass spectrometry (MS/MS) scans. DecoID provides a complementary, method-independent approach where database spectra are computationally mixed to match an experimentally acquired spectrum by using LASSO regression. We validated that DecoID increases the number of identified metabolites in MS/MS datasets from both data-independent and data-dependent acquisition without increasing the false discovery rate. We applied DecoID to publicly available data from the MetaboLights repository and to data from human plasma, where DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching. DecoID is compatible with any user-defined MS/MS database and provides automated searching for some of the largest MS/MS databases currently available.", "claims": [{"id": "claim-method", "statement": "DecoID uses non-negative LASSO regression24 to deconvolve any MS/MS spectrum into a linear combination of database spectra.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34239103", "locator": "sections[2] \"Results\" paragraph 2", "quote": "DecoID uses non-negative LASSO regression24 to deconvolve any MS/MS spectrum into a linear combination of database spectra."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All MS/MS data used in the evaluation of DecoID has been uploaded to the MetaboLights repository as study MTBLS2207 and is also available on the DecoID GitHub release (https://github.com/e-stan/DecoID/releases/). The publicly available dataset analyzed is available on MetaboLights as study MTBLS1066 (all reversed-phase negative mode datafiles were used). The MS/MS databases applied can be obtained at the curators’ websites (https://mona.fiehnlab.ucdavis.edu, https://www.mzcloud.org, and https://hmdb.ca). The in-house IROA metabolite database is available within the DecoID release on GitHub (https://github.com/e-stan/DecoID/releases/), and the reference spectra have been uploaded to MoNA (submitter: Ethan Stancliffe, origin file: IROA_DB_for_mona_filtered_exported_addedInfo.msp).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34239103", "locator": "sections[30] \"Data availability\" paragraph 2", "quote": "All MS/MS data used in the evaluation of DecoID has been uploaded to the MetaboLights repository as study MTBLS2207 and is also available on the DecoID GitHub release (https://github.com/e-stan/DecoID/releases/). The publicly available dataset analyzed is available on MetaboLights as study MTBLS1066 (all reversed-phase negative mode datafiles were used). The MS/MS databases applied can be obtained at the curators’ websites (https://mona.fiehnlab.ucdavis.edu, https://www.mzcloud.org, and https://hmdb.ca). The in-house IROA metabolite database is available within the DecoID release on GitHub (https://github.com/e-stan/DecoID/releases/), and the reference spectra have been uploaded to MoNA (submitter: Ethan Stancliffe, origin file: IROA_DB_for_mona_filtered_exported_addedInfo.msp)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching.", "kind": "quantitative", "target": {"value": 30.0, "unit": "per cent", "tolerance": null, "source": "We applied DecoID to publicly available data from the MetaboLights repository and to data from human plasma, where DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching."}, "evidence": [{"asset": "source:pmid:34239103", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We applied DecoID to publicly available data from the MetaboLights repository and to data from human plasma, where DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching.", "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:34239103"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34239103", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41592-021-01195-3", "sha256": "sha256:04c173ff3e03a6e54afa011e020a64fbedc63fec4ac036bf0bd3eb9f0841c511", "bytes": 56964, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41592-021-01195-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9302972", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "auROC"}}, {"id": "method-2", "family": null, "specific": null, "label": "non-negative LASSO regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DecoID uses non-negative LASSO regression24 to deconvolve any MS/MS spectrum into a linear combination of database spectra."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 30.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["All MS/MS data used in the evaluation of DecoID has been uploaded to the MetaboLights repository as study MTBLS2207 and is also available on the DecoID GitHub release (https://github.com/e-stan/DecoID/releases/). The publicly available dataset analyzed is available on MetaboLights as study MTBLS1066 (all reversed-phase negative mode datafiles were used). The MS/MS databases applied can be obtained at the curators’ websites (https://mona.fiehnlab.ucdavis.edu, https://www.mzcloud.org, and https://hmdb.ca). The in-house IROA metabolite database is available within the DecoID release on GitHub (https://github.com/e-stan/DecoID/releases/), and the reference spectra have been uploaded to MoNA (submitter: Ethan Stancliffe, origin file: IROA_DB_for_mona_filtered_exported_addedInfo.msp)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:34239103"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:02:26Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14362, "completion_tokens": 2843, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34239103", "type": "paper", "label": "pmid:34239103"}, {"id": "source:pmid:34239103", "type": "manuscript", "label": "PMID 34239103 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34239103", "type": "paper", "label": "pmid:34239103"}, {"id": "source:pmid:34239103", "type": "manuscript", "label": "PMID 34239103 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34239103", "type": "extraction", "used": ["source:pmid:34239103"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34239103", "parent_hash": "sha256:68089cdd1feb97010dba72690ecab110c1e6692bfbb623fabf1c6b40f45a14bb", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["os of precursor ions between multiple tandem mass spectrometry (MS/MS) scans. DecoID provides a complementa", "dditives for LC/MS from Millipore Sigma. The Mass Spectrometry Metabolite Library (IROA Technologies) was p"], "order_basis": "paper_text_order:387", "id": "assay:1"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["auROC"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}