GPMDB00145OtherSjostrom M, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human_femaleemma.nimeus@med.lu.se25944384Department of Biology, Institute of Molecular Systems Biology, et al.http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015591http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015590http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015589http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015582http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015581http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015584http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015583http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015586http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015585http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015588http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015587http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015481http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015480http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015479http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015593http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015472http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015592http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015471http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015595http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015474http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015473http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015594http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015597http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015476http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015475http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015596http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015478http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015599http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015477http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015598http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015490http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015492http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015491http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015483http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015482http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015485http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015484http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015487http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015486http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015489http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015488http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015494http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015493http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015496http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015495http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015498http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015497http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015499http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015708http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015707http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015700http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015702http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015701http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015704http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015703http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015706http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015705http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015609http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015608http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015601http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015600http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015603http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015602http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015605http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015604http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015607http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015606http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015619http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015612http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015611http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015614http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015613http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015616http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015615http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015618http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015617http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015610http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015509http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015502http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015623http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015622http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM323200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availableGPMDBIt is of highest importance to find proteins responsible for breast cancer dissemination, for use as biomarkers or treatment targets. We established and performed a combined nontargeted LC-MS/MS and a targeted LC-SRM workflow for discovery and validation of protein biomarkers. Eighty breast tumors, stratified for estrogen receptor status and development of distant recurrence (DR ± ), were collected. After enrichment of N-glycosylated peptides, label-free LC-MS/MS was performed on each individual tumor in triplicate. In total, 1515 glycopeptides from 778 proteins were identified and used to create a map of the breast cancer N-glycosylated proteome. Based on this specific proteome map, we constructed a 92-plex targeted label-free LC-SRM panel. These proteins were quantified across samples by LC-SRM, resulting in 10 proteins consistently differentially regulated between DR+/DR- tumors. Five proteins were further validated in a separate cohort as prognostic biomarkers at the gene expression level. We also compared the LC-SRM results to clinically reported HER2 status, demonstrating its clinical accuracy. In conclusion, we demonstrate a combined mass spectrometry strategy, at large scale on clinical samples, leading to the identification and validation of five proteins as potential biomarkers for breast cancer recurrence. All MS data are available via ProteomeXchange and PASSEL with identifiers PXD001685 and PASS00643.A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.Sjöström Martin M,Ossola Reto R,Breslin Thomas T,Rinner Oliver O,Malmström Lars L,Schmidt Alexander A,Aebersold Ruedi R,Malmström Johan J,Niméus Emma E,Sjöström Martin M, Ossola Reto R, Breslin Thomas T, Rinner Oliver O, Malmström Lars L, Schmidt Alexander A, Aebersold Ruedi R, Malmström Johan J, Niméus Emma EMass Spectrum Analysis, Carcinomas, BC, Mass Spectrum, Mammary Neoplasms, Human Mammary Neoplasm, Carcinoma, Carcinoma of breast NOS, Breast Neoplasm, Human Mammary, Analyses, Breast Neoplasms, NEOPL BREAST, Mammary Neoplasm, Carcinoma of breast NOS (disorder), Neoplasms, Mammary Carcinoma, carcinoma OF breast, Spectrometry, Human Mammary Carcinomas, Human Mammary Neoplasms, Spectrum Analyses, Tumor, Spectrum Analysis, Cancer of the Breast, Human, Spectroscopy, CA - Carcinoma of breast, Mammary Carcinomas, Breast Tumor, BREAST NEOPL, Breast Tumors, Breast Cancer, Mass, Neoplasm, Carcinoma of breast (disorder), Human Mammary Carcinoma, Cancer of Breast, Carcinoma of the Breast, Analysis, biological marker., Breast, Mammary carcinoma, Mass Spectrum Analyses, Mass Spectroscopy, Tumors, CancerLC-MS2, liquid chromatography tandem mass spectroscopy, Relapse, Human Mammary Neoplasm, Carcinoma, data, Carcinoma of breast NOS, SRM., MUTYH-Associated Polyposis, single-organism developmental process, SRML1, Breast Neoplasms, AP-1, Neoplasms, c-jun, Proteins, PAPT, LC-MS/MS, Gene, Human Mammary Neoplasms, Tumor, SPDSY, tumours, LC-MS-MS, NEOPL, Human, Multiple Reaction Monitoring, development, polypeptide, Polypeptides, LC/MS/MS, Mammary Carcinomas, Recrudescence, Breast Tumor, BREAST NEOPL, LC-MSMS, Protein, Neoplasm, Gene Products, Human Mammary Carcinoma, Carcinoma of the Breast, Relapses, Mammary carcinoma, MAP, Carcinomas, BC, Mammary Neoplasms, Junc, RUTBC3, rabGAPLP, Breast Neoplasm, Human Mammary, LCMSMS, MRM, NEOPL BREAST, Mammary Neoplasm, Recrudescences, Carcinoma of breast NOS (disorder), Mammary Carcinoma, Recurrences, carcinoma OF breast, Human Mammary Carcinomas, RabGAP-5, tumour, proteins, MYH-Associated Polyposis, free, Cancer of the Breast, RABGAP5, Protein Gene Products, AP1, CA - Carcinoma of breast, Gene Proteins, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), neoplasm of the breast, liquid chromatography-tandem mass spectroscopy, RUSC3, Breast Tumors, Breast Cancer, c-Jun, Carcinoma of breast (disorder), liquid chromatography tandem mass spectrometry, Cancer of Breast, Breast, Proteomes, NEOPLASMS BENIGN, Neoplastic Growth, Neoplasia, SPS1, Tumors, CancerMass Spectrum Analysis, Carcinomas, BC, Mass Spectrum, Mammary Neoplasms, Human Mammary Neoplasm, Carcinoma, Carcinoma of breast NOS, Breast Neoplasm, Human Mammary, Analyses, Breast Neoplasms, NEOPL BREAST, Mammary Neoplasm, Carcinoma of breast NOS (disorder), Neoplasms, Mammary Carcinoma, carcinoma OF breast, Spectrometry, Human Mammary Carcinomas, Human Mammary Neoplasms, Spectrum Analyses, Tumor, Spectrum Analysis, Cancer of the Breast, Human, Spectroscopy, CA - Carcinoma of breast, Mammary Carcinomas, Breast Tumor, BREAST NEOPL, Breast Tumors, Breast Cancer, Mass, Neoplasm, Carcinoma of breast (disorder), Human Mammary Carcinoma, Cancer of Breast, Carcinoma of the Breast, Analysis, biological marker., Breast, Mammary carcinoma, Mass Spectrum Analyses, Mass Spectroscopy, Tumors, Cancerliquid chromatography tandem mass spectroscopy, big, scale tissue, Carcinoma of breast NOS, Viral Marker, Biological Markers, Surrogate Endpoints, single-organism developmental process, Clinical Markers, Laboratory, SRML1, Breast Neoplasms, Clinical Marker, Neoplasms, peltate hair, Biochemical, Gene, Endpoint, Human Mammary Neoplasms, Spectrum Analyses, Tumor, Serum, LC-MS-MS, NEOPL, Human, Surrogate End Points, Surrogate Markers, Polypeptides, Laboratory Markers, large, Breast Tumor, Biological, BREAST NEOPL, LC-MSMS, Gene Products, Mass, Carcinoma of the Breast, Relapses, Analysis, Work Flow, MAP, Mass Spectroscopy, Mass Spectrum Analysis, BC, treatment, Mammary Neoplasms, rabGAPLP, Human Mammary, LCMSMS, Clinical, Gene Expressions, MRM, Analyses, Identification, Mammary Neoplasm, Recrudescences, Carcinoma of breast NOS (disorder), plant peltate hair, Mammary Carcinoma, Biological Marker, Recurrences, Human Mammary Carcinomas, RabGAP-5, proteins, tumour, Expressions, free, Cancer of the Breast, CA - Carcinoma of breast, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Immunologic Markers, Immune, Markers, neoplasm of the breast, RUSC3, data., Viral Markers, great, disease management, Carcinoma of breast (disorder), Expression, Breast, Immunologic Marker, Neoplastic Growth, Biologic, SPS1, Tumors, Cancer, LC-MS2, Relapse, Human Mammary Neoplasm, Carcinoma, use, Viral, MUTYH-Associated Polyposis, Surrogate Endpoint, Proteins, Serum Markers, PAPT, LC-MS/MS, End Point, Biochemical Markers, SPDSY, Biologic Marker, Spectrum Analysis, tumours, results, Immune Marker, Multiple Reaction Monitoring, Spectroscopy, polypeptide, development, LC/MS/MS, Workflows, Mammary Carcinomas, Recrudescence, Marker, Surrogate End Point, Protein, Neoplasm, Human Mammary Carcinoma, scales, Mammary carcinoma, Mass Spectrum Analyses, Biologic Markers, Carcinomas, Mass Spectrum, RUTBC3, Breast Neoplasm, Serum Marker, End Points, scale, NEOPL BREAST, Surrogate, SRM, carcinoma OF breast, Endpoints, Spectrometry, expanded, Identifications (Psychology), Immunologic, Laboratory Marker, MYH-Associated Polyposis, Surrogate Marker, RABGAP5, Protein Gene Products, Gene Proteins, enlarged, Biochemical Marker, liquid chromatography-tandem mass spectroscopy, Breast Tumors, Breast Cancer, liquid chromatography tandem mass spectrometry, Cancer of Breast, Proteomes, Work Flows, NEOPLASMS BENIGN, Neoplasia, Immune Markers1405http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320015681dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.004318322023442320.01.0falseA Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.Data from ProteomeXchange, PXD ID: PXD001685. File: B08-07165_c.mzml. Published as part of J Proteome Res. 2015 Jun 5 . From the Abstract: {{i} ... Eighty breast tumors, stratified for estrogen receptor status and development of distant recurrence (DR - ), were collected. After enrichment of N-glycosylated peptides, label-free LC-MS/MS was performed on each individual tumor in triplicate. In total, 1515 glycopeptides from 778 proteins were identified and used to create a map of the breast cancer N-glycosylated proteome. Based on this specific proteome map, we constructed a 92-plex targeted label-free LC-SRM panel ... {{/i}}2015-06-17GPM3232001568125944384PXD001685PXD001685