Variability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32119684", "kind": "science-record", "revision": 8, "content_hash": "sha256:6c1d6400d1b9cecf6e6c7011fd205b1d1e3eb19f093488cfdfe617e60e916163", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Variability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles.", "doi": "10.1371/journal.pone.0228871", "pmid": "32119684", "authors": ["Suma Tiruvayipati", "Don Wolfgeher", "Ming Yue", "FangFang Duan", "Jorge Andrade", "Hui Jiang", "Lucia Schuger"], "journal": "PloS one", "year": 2020, "abstract": "Exosomes are extracellular vesicles (EVs) of ~20-200 nm diameter that shuttle DNAs, RNAs, proteins and other biomolecules between cells. The large number of biomolecules present in exosomes demands the frequent use of high-throughput analysis. This, in turn, requires technical replicates (TRs), and biological replicates (BRs) to produce accurate results. As the number and abundance of identified biomolecules varies between replicates (Rs), establishing the replicate variability predicted for the event under study is essential in determining the number of Rs required. Although there have been few reports of replicate variability in high throughput biological data, none of them focused on exosomes. Herein, we determined the replicate variability in protein profiles found in exosomes released from 3 lung adenocarcinoma cell lines, H1993, A549 and H1975. Since exosome isolates are invariably contaminated by a small percentage of ~200-300 nm microvesicles, we refer to our samples as exosome-enriched EVs (EE-EVs). We generated BRs of EE-EVs from each cell line, and divided each group into 3 TRs. All Rs were analyzed by liquid chromatography/mass spectrometry (LC/MS/MS) and customized bioinformatics and biostatistical workflows (raw data available via ProteomeXchange: PXD012798). We found that the variability among TRs as well as BRs, was largely qualitative (protein present or absent) and higher among BRs. By contrast, the quantitative (protein abundance) variability was low, save for the H1975 cell line where the quantitative variability was significant. Importantly, our replicate strategy identified 90% of the most abundant proteins, thereby establishing the utility of our approach.", "claims": [{"id": "claim-method", "statement": "One-way repeated measures analysis of variance (ANOVA) was conducted to check for statistically significant differences in the means of proteins levels of TRs, BRs, and the 9 Rs of all the cell lines.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32119684", "locator": "sections[9] \"Biostatistical analysis\" paragraph 14", "quote": "One-way repeated measures analysis of variance (ANOVA) was conducted to check for statistically significant differences in the means of proteins levels of TRs, BRs, and the 9 Rs of all the cell lines."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE [33] partner repository with the dataset identifier PXD012798 and 10.6019/PXD012798.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32119684", "locator": "sections[5] \"Proteomic analysis\" paragraph 5", "quote": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE [33] partner repository with the dataset identifier PXD012798 and 10.6019/PXD012798."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32119684"], "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:32119684", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0228871", "sha256": "sha256:d0fff970adc582c1626e9362044daf2cfb22ff301f56e56f8dd7aae95f6214a6", "bytes": 38885, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0228871", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7051218", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32119684:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dd3588d9977e54eb3a89c6afe9c784acb58192ec1c2923d8ab55522ec8e39e1a", "bytes": 347, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#pone.0228871.t001", "version": null, "note": "Table shows one-way repeated measures ANOVA F-values and corresponding p-values for the levels of proteins identified in EE-EVs in 3 TRs and 3 BRs for H1993, A549 and H1975 cell lines.", "structure": {"pmcid": "PMC7051218", "section_index": 15, "section_title": "Quantitative variability analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Table shows one-way repeated measures ANOVA F-values and corresponding p-values for the levels of proteins identified in EE-EVs in 3 TRs and 3 BRs for H1993, A549 and H1975 cell lines.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[15]/table-wrap[1]#pone.0228871.t001"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "One-way repeated measures analysis of variance (ANOVA) was conducted to check for statistically significant differences in the means of proteins levels of TRs, BRs, and the 9 Rs of all the cell lines."}}], "targets": [], "gaps": []}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Since exosome isolates are invari", "9 (ATCC CCL-185). H1975 and H1993 cells were cultured in RPMI media (Gibco, 11875119) while, A549 cel", "dia (Gibco, 11875119) while, A549 cells were cultured in Ham’s F-12K media (Corning, 10-025-CV) with", "3 (ATCC CRL-5909), H1975 (ATCC CRL-5908) and A549 (ATCC CCL-185). 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