DDASSQ: An open-source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34312990", "kind": "science-record", "revision": 6, "content_hash": "sha256:ead0d698f3c5e6455e4e53f3cc2aba95eda73dfcf6a74495eaa75a9a8016eb8e", "created_at": "2026-11-01T15:41:45Z", "updated_at": "2026-11-01T21:25:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DDASSQ: An open-source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform.", "doi": "10.1002/pmic.202000319", "pmid": "34312990", "authors": ["Monika Svecla", "Giulia Garrone", "Fiorenza Faré", "Giacomo Aletti", "Giuseppe Danilo Norata", "Giangiacomo Beretta"], "journal": "Proteomics", "year": 2021, "abstract": "In this study we investigated the performance of a computational pipeline for protein identification and label free quantification (LFQ) of LC-MS/MS data sets from experimental animal tissue samples, as well as the impact of its specific peptide search combinatorial approach. The full pipeline workflow was composed of peptide search engine adapters based on different identification algorithms, in the frame of the open-source OpenMS software running within the KNIME analytics platform. Two different in silico tryptic digestion, database-search assisted approaches (X!Tandem and MS-GF+), de novo peptide sequencing based on Novor and consensus library search (SpectraST), were tested for the processing of LC-MS/MS raw data files obtained from proteomic LC-MS experiments done on proteolytic extracts from mouse ex vivo liver samples. The results from proteomic LFQ were compared to those based on the application of the two software tools MaxQuant and Proteome Discoverer for protein inference and label-free data analysis in shotgun proteomics. Data are available via ProteomeXchange with identifier PXD025097.", "claims": [{"id": "claim-method", "statement": "The log‐transformed data showed significant correlation between the DDASSQ LFQ‐Δ values with those from PD (R = 0.948, p < 0.001, Pearson product‐moment, two‐sided, Figure 6C) and MQ (R = 0.907, p < 0.001, Pearson product‐moment, two‐sided, Figure 6D), respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34312990", "locator": "sections[8] \"DDASSQ/PD/MQ LFQ correlation results\" paragraph 5", "quote": "The log‐transformed data showed significant correlation between the DDASSQ LFQ‐Δ values with those from PD (R = 0.948, p < 0.001, Pearson product‐moment, two‐sided, Figure 6C) and MQ (R = 0.907, p < 0.001, Pearson product‐moment, two‐sided, Figure 6D), respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in PRIDE repository with reference number PXD025097, at http://www.ebi.ac.uk/pride/archive/projects/PXD002099 with reference number PXD002099, and at the URL https://cptac‐data‐portal.georgetown.edu/cptac/study/showDetails/10424 (sample set Orbi2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34312990", "locator": "sections[26] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are openly available in PRIDE repository with reference number PXD025097, at http://www.ebi.ac.uk/pride/archive/projects/PXD002099 with reference number PXD002099, and at the URL https://cptac‐data‐portal.georgetown.edu/cptac/study/showDetails/10424 (sample set Orbi2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34312990"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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