A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35354825", "kind": "science-record", "revision": 3, "content_hash": "sha256:cceaed1812fef56ba26b83c65b345e3aced03ade6fdfb0afebcc5dd019c3a2e5", "created_at": "2026-11-01T18:14:09Z", "updated_at": "2026-11-01T21:27:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.", "doi": "10.1038/s41597-022-01216-6", "pmid": "35354825", "authors": ["Bart Van Puyvelde", "Simon Daled", "Sander Willems", "Ralf Gabriels", "Anne Gonzalez de Peredo", "Karima Chaoui", "Emmanuelle Mouton-Barbosa", "David Bouyssié", "Kurt Boonen", "Christopher J Hughes", "Lee A Gethings", "Yasset Perez-Riverol", "Nic Bloomfield", "Stephen Tate", "Odile Schiltz", "Lennart Martens", "Dieter Deforce", "Maarten Dhaenens"], "journal": "Scientific data", "year": 2022, "abstract": "In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).", "claims": [{"id": "claim-method", "statement": "Next, the differences in the fragmentation process between the instruments (all of which are beam-type CID) can be assessed by mutually mapping the MS2 intensities.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35354825", "locator": "sections[34] \"Raw data\" paragraph 2", "quote": "Next, the differences in the fragmentation process between the instruments (all of which are beam-type CID) can be assessed by mutually mapping the MS2 intensities."}], "state": "complete"}, {"id": "claim-data-access", "statement": "MS2PIP is open source, licensed under the Apache-2.0 License, and hosted on https://github.com/compomics/ms2pip_c. 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