A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.

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The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).", "claims": [{"id": "claim-method", "statement": "Adjusted p-values were computed using the Benjamini-Hochberg method prior to filtering", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37833331", "locator": "sections[14] \"Proteome differential expression analysis\" paragraph 2", "quote": "Adjusted p-values were computed using the Benjamini-Hochberg method prior to filtering"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Code to perform PCA, generate heat maps and volcano plots, and carry out the transcriptome differential expression analysis is publicly available under repository https://github.com/alanlorenzetti/protDynContGenExp_v2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37833331", "locator": "sections[30] \"Code availability\" paragraph 2", "quote": "Code to perform PCA, generate heat maps and volcano plots, and carry out the transcriptome differential expression analysis is publicly available under repository https://github.com/alanlorenzetti/protDynContGenExp_v2."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports a comprehensive H. salinarum NRC-1 spectral assay library containing 21,074 distinct peptides that represent 97% of the predicted proteome.", "kind": "quantitative", "target": {"value": 97.0, "unit": "per cent", "tolerance": null, "source": "The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon."}, "evidence": [{"asset": "source:pmid:37833331", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports a comprehensive H. salinarum NRC-1 spectral assay library containing 21,074 distinct peptides that represent 97% of the predicted proteome.", "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:37833331"], "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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