A framework for quality control in quantitative proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38645098", "kind": "science-record", "revision": 3, "content_hash": "sha256:9f2f35f69036be80974d0bbd95dc52322ab49769b77c7171e607588cf6ea0a1f", "created_at": "2026-11-01T19:20:36Z", "updated_at": "2026-11-01T21:32:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A framework for quality control in quantitative proteomics.", "doi": "10.1101/2024.04.12.589318", "pmid": "38645098", "authors": ["Kristine A Tsantilas", "Gennifer E Merrihew", "Julia E Robbins", "Richard S Johnson", "Jea Park", "Deanna L Plubell", "Jesse D Canterbury", "Eric Huang", "Michael Riffle", "Vagisha Sharma", "Brendan X MacLean", "Josh Eckels", "Christine C Wu", "Michael S Bereman", "Sandra E Spencer", "Andrew N Hoofnagle", "Michael J MacCoss"], "journal": "bioRxiv : the preprint server for biology", "year": 2024, "abstract": "A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and on ProteomeXchange under the identifier PXD051318.", "claims": [{"id": "claim-method", "statement": "The coefficient of variation (CV) calculated for all peptides in the inter-batch QC improved 6.3% after normalization and batch adjustment at the peptide-level and 16.9% at the protein level.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645098", "locator": "sections[16] \"Assessing Quantitative Results\" paragraph 3", "quote": "The coefficient of variation (CV) calculated for all peptides in the inter-batch QC improved 6.3% after normalization and batch adjustment at the peptide-level and 16.9% at the protein level."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw files (DIA, PRM, DDA), Skyline documents, processed results (DIA, PRM) used as input for figure generation, FASTA files, EncyclopeDIA files, metadata, and the large input files (>25 MB) for R scripts are available on PanoramaWeb (panoramaweb.org/maccoss-sample-qc-system-suitability.url) and registered via the ProteomeXchange with identifier PXD051318. The processed DDA results in Figure 3 are accessible on Limelight62 under the identifier Project 131. The input files <25 MB and the R code to generate Figures 3–6 (maccoss_qc_figures_3_4_5_6_S1.Rmd) and Figure 7 (plot_7a.r, plot_7b.r) are available for download on GitHub under an Apache 2.0 license: (github.com/uw-maccosslab/manuscript-qc-system-suitability/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645098", "locator": "sections[10] \"Data Accessibility and Figure Generation\" paragraph 2", "quote": "Raw files (DIA, PRM, DDA), Skyline documents, processed results (DIA, PRM) used as input for figure generation, FASTA files, EncyclopeDIA files, metadata, and the large input files (>25 MB) for R scripts are available on PanoramaWeb (panoramaweb.org/maccoss-sample-qc-system-suitability.url) and registered via the ProteomeXchange with identifier PXD051318. The processed DDA results in Figure 3 are accessible on Limelight62 under the identifier Project 131. The input files <25 MB and the R code to generate Figures 3–6 (maccoss_qc_figures_3_4_5_6_S1.Rmd) and Figure 7 (plot_7a.r, plot_7b.r) are available for download on GitHub under an Apache 2.0 license: (github.com/uw-maccosslab/manuscript-qc-system-suitability/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After normalization and batch adjustment, the coefficient of variation of all peptides in the inter-batch QC improved by 6.3% at the peptide level and 16.9% at the protein level.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38645098", "locator": "sections[16] \"Assessing Quantitative Results\" paragraph 3", "quote": "The coefficient of variation (CV) calculated for all peptides in the inter-batch QC improved 6.3% after normalization and batch adjustment at the peptide-level and 16.9% at the protein level."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "After normalization and batch adjustment, the coefficient of variation of all peptides in the inter-batch QC improved by 6.3% at the peptide level and 16.9% at the protein level.", "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:38645098"], "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_unresolved", "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": ["data:geo:PXD051318"], "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": ["data:geo:PXD051318"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38645098", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1101/2024.04.12.589318", "sha256": "sha256:edf98fe2de2d5385b75de0c185c4c32624c3943141e71be6fdd6ddeee24f2ac3", "bytes": 58197, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1101/2024.04.12.589318", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11030400", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD051318", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD051318", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD051318", "version": null, "note": "Raw files (DIA, PRM, DDA), Skyline documents, processed results (DIA, PRM) used as input for figure generation, FASTA files, EncyclopeDIA files, metadata, and the large input files (>25 MB) for R scripts are available on PanoramaWeb (panoramaweb.org/maccoss-sample-qc-system-suitability.url) and registered via the ProteomeXchange with identifier PXD051318. The processed DDA results in Figure 3 are accessible on Limelight62 under the identifier Project 131. The input files <25 MB and the R code to generate Figures 3–6 (maccoss_qc_figures_3_4_5_6_S1.Rmd) and Figure 7 (plot_7a.r, plot_7b.r) are available for download on GitHub under an Apache 2.0 license: (github.com/uw-maccosslab/manuscript-qc-system-suitability/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw files (DIA, PRM, DDA), Skyline documents, processed results (DIA, PRM) used as input for figure generation, FASTA files, EncyclopeDIA files, metadata, and the large input files (>25 MB) for R scripts are available on PanoramaWeb (panoramaweb.org/maccoss-sample-qc-system-suitability.url) and registered via the ProteomeXchange with identifier PXD051318. The processed DDA results in Figure 3 are accessible on Limelight62 under the identifier Project 131. The input files <25 MB and the R code to generate Figures 3–6 (maccoss_qc_figures_3_4_5_6_S1.Rmd) and Figure 7 (plot_7a.r, plot_7b.r) are available for download on GitHub under an Apache 2.0 license: (github.com/uw-maccosslab/manuscript-qc-system-suitability/).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD051318 not downloaded", "asset:data:geo:PXD051318 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Coefficient of variation (CV)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The coefficient of variation (CV) calculated for all peptides in the inter-batch QC improved 6.3% after normalization and batch adjustment at the peptide-level and 16.9% at the protein level."}}], "targets": [], "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": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Coefficient of variation (CV)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD051318"], "resolved_accessions": [], "statements": ["Raw files (DIA, PRM, DDA), Skyline documents, processed results (DIA, PRM) used as input for figure generation, FASTA files, EncyclopeDIA files, metadata, and the large input files (>25 MB) for R scripts are available on PanoramaWeb (panoramaweb.org/maccoss-sample-qc-system-suitability.url) and registered via the ProteomeXchange with identifier PXD051318. The processed DDA results in Figure 3 are accessible on Limelight62 under the identifier Project 131. The input files <25 MB and the R code to generate Figures 3–6 (maccoss_qc_figures_3_4_5_6_S1.Rmd) and Figure 7 (plot_7a.r, plot_7b.r) are available for download on GitHub under an Apache 2.0 license: (github.com/uw-maccosslab/manuscript-qc-system-suitability/)."], "basis": "The paper names PXD051318, but the accession does not resolve in the repository (not_in_proteomexchange), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38645098", "data:geo:PXD051318"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD051318"]}, "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": "2026-11-01T19:16:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13465, "completion_tokens": 2319, "cached_tokens": 128}}, "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:38645098", "type": "paper", "label": "pmid:38645098"}, {"id": "source:pmid:38645098", "type": "manuscript", "label": "PMID 38645098 full text"}, {"id": "data:geo:PXD051318", "type": "dataset", "label": "GEO PXD051318"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38645098", "type": "paper", "label": "pmid:38645098"}, {"id": "source:pmid:38645098", "type": "manuscript", "label": "PMID 38645098 full text"}, {"id": "data:geo:PXD051318", "type": "dataset", "label": "GEO PXD051318"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38645098", "type": "extraction", "used": ["source:pmid:38645098"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD051318", "type": "accession_resolution", "used": ["data:geo:PXD051318"], "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:38645098", "parent_hash": "sha256:4833d44ac8ce95f6cbfb2a7bbd50dbd53bab0a69bea9419fd5049eddc9b94412", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD051318 licence not read", "asset:data:geo:PXD051318 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "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": ["ramework for quality control in quantitative proteomics.", "eproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workfl", "ocol-specific rather than a problem with the LC-MS/MS system. The instrument operator initially po"], "order_basis": "paper_text_order:3", "id": "assay:1"}]}