Quantitative N-glycoproteomics reveals altered glycosylation levels of various plasma proteins in bloodstream infected patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29596458", "kind": "science-record", "revision": 6, "content_hash": "sha256:5fc4845cb5493b1f1a250ef901e727b32fe6161e58a3737fe1e0d395695f9b1e", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:21:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative N-glycoproteomics reveals altered glycosylation levels of various plasma proteins in bloodstream infected patients.", "doi": "10.1371/journal.pone.0195006", "pmid": "29596458", "authors": ["Sakari Joenvaara", "Mayank Saraswat", "Pentti Kuusela", "Shruti Saraswat", "Rahul Agarwal", "Johanna Kaartinen", "Asko Järvinen", "Risto Renkonen"], "journal": "PloS one", "year": 2018, "abstract": "Bloodstream infections are associated with high morbidity and mortality with rates varying from 10-25% and higher. Appropriate and timely onset of antibiotic therapy influences the prognosis of these patients. It requires the diagnostic accuracy which is not afforded by current gold standards such as blood culture. Moreover, the time from blood sampling to blood culture results is a key determinant of reducing mortality. No established biomarkers exist which can differentiate bloodstream infections from other systemic inflammatory conditions. This calls for studies on biomarkers potential of molecular profiling of plasma as it is affected most by the molecular changes accompanying bloodstream infections. N-glycosylation is a post-translational modification which is very sensitive to changes in physiology. Here we have performed targeted quantitative N-glycoproteomics from plasma samples of patients with confirmed positive blood culture together with age and sex matched febrile controls with negative blood culture reports. Three hundred and sixty eight potential N-glycopeptides were quantified by mass spectrometry and 149 were further selected for identification. Twenty four N-glycopeptides were identified with high confidence together with elucidation of the peptide sequence, N-glycosylation site, glycan composition and proposed glycan structures. Principal component analysis, orthogonal projections to latent structures-discriminant analysis (S-Plot) and self-organizing maps clustering among other statistical methods were employed to analyze the data. These methods gave us clear separation of the two patient classes. We propose high-confidence N-glycopeptides which have the power to separate the bloodstream infections from blood culture negative febrile patients and shed light on host response during bacteremia. Data are available via ProteomeXchange with identifier PXD009048.", "claims": [{"id": "claim-method", "statement": "To further identify the features (Ions) which can classify the cases vs controls, the data was used to perform the orthogonal projections to latent structures-discriminant analysis (OPLS-DA). This modeling of the data gave us the S-Plot which is shown in Fig 3.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29596458", "locator": "sections[5] \"HDMSE and statistical analysis\" paragraph 5", "quote": "To further identify the features (Ions) which can classify the cases vs controls, the data was used to perform the orthogonal projections to latent structures-discriminant analysis (OPLS-DA). This modeling of the data gave us the S-Plot which is shown in Fig 3."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry N-glycoproteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [35] partner repository with the dataset identifier PXD009048. Additional relevant data are within the paper and its Supporting Information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29596458", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry N-glycoproteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [35] partner repository with the dataset identifier PXD009048. Additional relevant data are within the paper and its Supporting Information files."}], "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:29596458"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD009048"], "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:PXD009048"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29596458", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0195006", "sha256": "sha256:cc3375503270b60c4d11386575812b01cc37f9a0c822d1a5892a0206081b3ecd", "bytes": 50514, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0195006", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5875812", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD009048", "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=PXD009048", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD009048", "version": null, "note": "The mass spectrometry N-glycoproteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [35] partner repository with the dataset identifier PXD009048. Additional relevant data are within the paper and its Supporting Information files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry N-glycoproteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [35] partner repository with the dataset identifier PXD009048. Additional relevant data are within the paper and its Supporting Information files.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Bloodstream infection N-glycoproteomics", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29596458:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:243308d79787025d0d2fc2ad2885f3531e471df656a361e3f9207772a3f612a9", "bytes": 3418, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#pone.0195006.t001", "version": null, "note": "Identified N-glycopeptides.m/z values of the N-glycopeptides, cgharrge, Uniport Id, peptide mass, N-glycosylation site, peptide sequence, Glycan composition, porposed annotated structure, N-glycopeptide scores and area under the curve (AUC) values from Receiver operating curve analysis of these N-glycopeptides are given in the table. Where a structure was not matched with database and was elucidated de novo, it is written as denovo (see methods and references therein for more details).", "structure": {"pmcid": "PMC5875812", "section_index": 6, "section_title": "Identification of N-glycopeptides", "row_count": 25, "column_count": 10}, "table": {"label": "Table 1", "caption": "Identified N-glycopeptides.m/z values of the N-glycopeptides, cgharrge, Uniport Id, peptide mass, N-glycosylation site, peptide sequence, Glycan composition, porposed annotated structure, N-glycopeptide scores and area under the curve (AUC) values from Receiver operating curve analysis of these N-glycopeptides are given in the table. Where a structure was not matched with database and was elucidated de novo, it is written as denovo (see methods and references therein for more details).", "rows": [["m/z", "Charge", "Protein Uniprot Id", "Peptide_Mass", "N_site", "Peptide Sequence", "Glycan composition", "Proposed Glycan Structure", "Score", "AUC from ROC curve analysis"], ["990.9476", "4", "A1AT_HUMAN", "1754.888", "271", "YLGNATAIFFLPDEGK", "S2H5N4", "SHNH(SHNH)HNN", "77.59", "0.860"], ["1011.432", "4", "A1AT_HUMAN", "1754.888", "271", "YLGNATAIFFLPDEGK", "S2H3N6", "denovo", "44.72", "0.857"], ["1320.927", "3", "A1AT_HUMAN", "1754.888", "271", "YLGNATAIFFLPDEGK", "S2H5N4", "SHNH(SHNH)HNN", "70.66", "0.884"], ["1068.449", "4", "CERU_HUMAN", "1891.834", "138", "EHEGAIYPDNTTDFQR", "H5N7F1", "denovo", "40.55", "0.774"], ["1067.238", "5", "CGAT1_HUMAN", "2316.176", "324", "AANFRNFTFIQLNGEFSRGK", "S2H10N4", "denovo", "28.54", "0.782"], ["903.1394", "4", "HEMO_HUMAN", "1403.674", "187", "SWPAVGNCSSALR", "S2H5N4", "SHNH(SHNH)HNN", "51.02", "0.568"], ["939.653", "4", "HEMO_HUMAN", "1403.674", "187", "SWPAVGNCSSALR", "S2H5N4F1", "SHNH(SHNH)HN(F)N", "46.03", "0.753"], ["985.9345", "4", "HEMO_HUMAN", "1734.885", "453", "ALPQPQNVTSLLGCTH", "S2H5N4", "SHNH(SHNH)HNN", "39.93", "0.787"], ["1203.814", "3", "HEMO_HUMAN", "1403.674", "187", "SWPAVGNCSSALR", "S2H5N4", "SHNH(SHNH)HNN", "77.43", "0.596"], ["932.0305", "5", "HPT_HUMAN", "1794.004", "241", "VVLHPNYSQVDIGLIK", "S3H6N5", "SHNH(SHN(SHN)H)HNN", "39.03", "0.887"], ["1092.015", "4", "HPT_HUMAN", "1794.004", "241", "VVLHPNYSQVDIGLIK", "S2H6N5", "SHNH(SHN(HN)H)HNN", "39.04", "0.764"], ["1115.226", "3", "HPT_HUMAN", "1794.004", "241", "VVLHPNYSQVDIGLIK", "S1H4N3", "SHNH(H)HNN", "58.34", "0.900"], ["1225.552", "4", "HPT_HUMAN", "1794.004", "241", "VVLHPNYSQVDIGLIK", "S2H10N3F2", "denovo", "42.13", "0.641"], ["1333.97", "3", "HPT_HUMAN", "1794.004", "241", "VVLHPNYSQVDIGLIK", "S2H5N4", "SHNH(SHNH)HNN", "74.33", "0.910"], ["916.6563", "4", "HPTR_HUMAN", "1457.726", "149,153", "NLFLNHSENATAK", "S2H5N4", "SHNH(SHNH)HNN", "64.48", "0.868"], ["885.6227", "5", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "H4N4", "HNH(NH)HNN", "29.79", "0.767"], ["976.2765", "5", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "S1H5N4", "SHNH(HNH)HNN", "36.56", "0.618"], ["984.488", "5", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "S1H4N5", "SHNH(NH)(N)HNN", "54.39", "0.789"], ["1016.904", "5", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "S1H5N5", "SHN(HN)H(NH)HNN", "64.97", "0.954"], ["1147.326", "4", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "H5N4", "HNH(HNH)HNN", "33.31", "0.723"], ["1179.592", "4", "IGHA1_HUMAN", "2962.604", "144", "LSLHRPALEDLLLGSEANLTCTLTGLR", "S1H4N4", "SHNH(NH)HNN", "60.04", "0.713"], ["868.048", "3", "IGHG2_HUMAN", "1156.515", "176", "EEQFNSTFR", "H3N4F1", "NH(NH)HN(F)N", "85.11", "0.767"], ["885.1539", "4", "IGHG2_HUMAN", "1638.811", "176", "TKPREEQFNSTFR", "S1H4N4F1", "SHNH(NH)HN(F)N", "42.52", "0.856"], ["989.7621", "3", "IGHG2_HUMAN", "1156.515", "176", "EEQFNSTFR", "H4N5F1", "NNH(HNH)HN(F)N", "62.53", "0.623"]], "row_count": 25, "column_count": 10, "numeric_cells": 146, "header_rows": 1, "locator": "section[6]/table-wrap[1]#pone.0195006.t001"}}], "gaps": ["asset:data:geo:PXD009048 not downloaded", "asset:data:geo:PXD009048 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Principal component analysis"}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-3", "family": null, "specific": null, "label": "Orthogonal projections to latent structures-discriminant analysis (OPLS-DA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To further identify the features (Ions) which can classify the cases vs controls, the data was used to perform the orthogonal projections to latent structures-discriminant analysis (OPLS-DA). 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