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To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs."],"pubmed_title":["Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering."],"pubmed_authors":["Hill Ryan C RC,Calle Elizabeth A EA,Dzieciatkowska Monika M,Niklason Laura E LE,Hansen Kirk C KC,","Hill Ryan C RC, Calle Elizabeth A EA, Dzieciatkowska Monika M, Niklason Laura E LE, Hansen Kirk C KC"],"name_synonyms":["brown rat, \"Gunn rats\" RELATED misnomer [], \"rats\" EXACT common_name [], pulmo, Tissue., Proteins, Engineering, lung parenchyma, \"brown rat\" EXACT common_name [], \"Rattus norvegicus8\" RELATED misspelling [], lungs, rats, Matrix Proteins, Extracellular Matrix, rat, Rattus sp. strain Wistar, Rats, Rattus norwegicus, parenchyma of lung, Mammals, \"Rattus rattiscus\" RELATED misnomer [], \"Norway rat\" EXACT genbank_common_name [], Extracellular, \"Rattus norwegicus\" RELATED misspelling [], \"rat\" EXACT common_name [], \"Rattus sp. strain Wistar\" EXACT equivalent_name [], Norway rat, Lungs, Rattus rattiscus, Entire lung, Gunn rats, Rattus norvegicus8"],"description_synonyms":["close to, Intervention Strategies, data, nucleocytoplasm, pulmo, Procedures, determination, Proteins, lung parenchyma, Matrix, Gene, Procedure, lungs, Matrices, extracted material, element, EMILIN4, Intervention or Procedure, near to, polypeptide, Polypeptides, method, soluble, Method, parenchyma of lung, method used in an experiment, chemical analysis, Protein, Studies, Gene Products, Extracellular Matrices, internal to cell, organ, insoluble, protoplasm, Intervention, protoplast, interventionDescription, Engineerings, Tissue, Interventional, proteins, Methodological, Methodological Study, plan specification, Protein Gene Products, Study, Gene Proteins, GPIa*, Methodological Studies, anatomical unit, approaches, SURGICAL AND MEDICAL PROCEDURES., Extracellular, body organ, vicinity of, ECM, Lungs, assay, Entire lung, MMRN, proteinaceous extracellular matrix"],"pubmed_title_synonyms":["brown rat, \"Gunn rats\" RELATED misnomer [], \"rats\" EXACT common_name [], pulmo, Tissue., Proteins, Engineering, lung parenchyma, \"brown rat\" EXACT common_name [], \"Rattus norvegicus8\" RELATED misspelling [], lungs, rats, Matrix Proteins, Extracellular Matrix, rat, Rattus sp. strain Wistar, Rats, Rattus norwegicus, parenchyma of lung, Mammals, \"Rattus rattiscus\" RELATED misnomer [], \"Norway rat\" EXACT genbank_common_name [], Extracellular, \"Rattus norwegicus\" RELATED misspelling [], \"rat\" EXACT common_name [], \"Rattus sp. strain Wistar\" EXACT equivalent_name [], Norway rat, Lungs, Rattus rattiscus, Entire lung, Gunn rats, Rattus norvegicus8"],"pubmed_abstract_synonyms":["Proteoglycan, glicoproteinas, close to, Intervention Strategies, use, nucleocytoplasm, pulmo, Procedures, determination, Proteins, lung parenchyma, Matrix, Gene, future organ, Procedure, lungs, compositionality, Matrices, composed of, extracted material, results, EMILIN4, element, Intervention or Procedure, Regenerative, near to, polypeptide, Polypeptides, organ field, method, Glycoprotein, soluble, glycoproteins, Drives., Method, parenchyma of lung, method used in an experiment, chemical analysis, Protein, Studies, Gene Products, Proteoglycan Type H, tissue portion, field, simple tissue, techniques, Extracellular Matrices, internal to cell, glycoproteine, organ, insoluble, protoplasm, Intervention, glicoproteina, portion of tissue, Glykoprotein, protoplast, interventionDescription, Engineerings, developmental field, content, Tissue, glycoproteines, Interventional, composition, proteins, Methodological, procedures, Methodological Study, SURGICAL AND MEDICAL PROCEDURES, plan specification, Protein Gene Products, Study, Gene Proteins, GPIa*, Methodological Studies, anatomical unit, approaches, Extracellular, ECM, body organ, vicinity of, structure, [glycoprotein], Regenerative Medicines, Medicine, Lungs, Medicines, assay, Entire lung, MMRN, proteinaceous extracellular matrix, methodology, Glykoproteine, Neoglycoproteins"],"view_count":["28"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310006954"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","project~0","pride~1","human_diseases~0","geo_datasets~0","embl~0","treefam~0","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","pride 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File: 20121108_Native_Frac3_Lung01_Run03.mzml. Published as part of  . From the Abstract: {{i}} ... To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions, and using recombinantly generated stable isotope labeled peptides for absolute quantification. Using this approach, we have generated seventy-four peptides, representing fifty-six proteins to quantify protein in native (non-decellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure ... {{/i}}","dates":{"submission":"2015-02-21"},"accession":"GPM32310006954","cross_references":{"pubmed":["25660013"],"Pride":["PXD001213"],"pride":[],"Pride Archive":["PXD001213"]}}