PeptideAtlasKentsis A, Monigatti F, Dorff K, Campagne F, Bachur R, Steen HTPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=6311'ude.dravrah.snerdlihc@neets.onnahOthersPeptideAtlasProteomicsLTQ OrbitrapHomo Sapiens (human)Knowledge of the biologically relevant components of human tissues has enabled the invention of numerous clinically useful diagnostic tests, as well as non-invasive ways of monitoring disease and its response to treatment. Recent use of advanced MS-based proteomics revealed that the composition of human urine is more complex than anticipated. Here, we extend the current characterization of the human urinary proteome by extensively fractionating urine using ultra-centrifugation, gel electrophoresis, ion exchange and reverse-phase chromatography, effectively reducing mixture complexity while minimizing loss of material. By using high-accuracy mass measurements of the linear ion trap-Orbitrap mass spectrometer and LC-MS/MS of peptides generated from such extensively fractionated specimens, we identified 2362 proteins in routinely collected individual urine specimens, including more than 1000 proteins not described in previous studies. Many of these are biomedically significant molecules, including glomerularly filtered cytokines and shed cell surface molecules, as well as renally and urogenitally produced transporters and structural proteins. Annotation of the identified proteome reveals distinct patterns of enrichment, consistent with previously described specific physiologic mechanisms, including 336 proteins that appear to be expressed by a variety of distal organs and glomerularly filtered from serum. Comparison of the proteomes identified from 12 individual specimens revealed a subset of generally invariant proteins, as well as individually variable ones, suggesting that our approach may be used to study individual differences in age, physiologic state and clinical condition. Consistent with this, annotation of the identified proteome by using machine learning and text mining exposed possible associations with 27 common and more than 500 rare human diseases, establishing a widely useful resource for the study of human pathophysiology and biomarker discovery.Urine proteomics for profiling of human disease using high accuracy mass spectrometry.Kentsis Alex A, Monigatti Flavio F, Dorff Kevin K, Campagne Fabien F, Bachur Richard R, Steen Hanno HMass Spectrum Analysis, Mass Spectrum, other disease, urinary levels, human disease, Analyses, Peptidomics, disorders, Spectrometry, medical condition, Spectrum Analyses, Spectrum Analysis, non-neoplastic, Spectroscopy, disease, MS, diseases, urinary aspects, Mass, Mass., disease or disorder, condition, disorder, diseases and disorders, Homo sapiens disease, Analysis, Mass Spectrum Analyses, Mass Spectroscopynon-neoplastic, other disease, disease, Perforated Appendicitis, acute appendicitis with generalized peritonitis, urinary levels, human disease, Appendicitis, diseases, urinary aspects, Peptidomics, Perforated, acute appendicitis with generalised peritonitis., disease or disorder, disorders, condition, disorder, Ruptured, diseases and disorders, Homo sapiens disease, Ruptured Appendicitis, acute appendicitis, medical condition, acute appendicitis with peritoneal abscessRuptured, Perforated Appendicitis, Ruptured Appendicitis, acute appendicitis with generalized peritonitis, urinary levels, acute appendicitis, Appendicitis, acute appendicitis with peritoneal abscess, urinary aspects, Perforated, acute appendicitis with generalised peritonitis.liquid chromatography tandem mass spectroscopy, other disease, Biological Markers, Viral Marker, human being, Surrogate Endpoints, Peptidomics, Clinical Markers, Laboratory, Clinical Marker, Blood, Mining, Preadmission, Biochemical, FBN, Gene, Endpoint, neutral molecular compounds, Serum, Routine Admission Test, LC-MS-MS, cell associated, Human, Surrogate End Points, Polypeptides, Surrogate Markers, Laboratory Markers, Electrophoreses, peptido, Homo sapiens, diseases, ECTOL1, Biological, Associations, LC-MSMS, Exchange, Gene Products, disease or disorder, DGS, Hospital Admission Tests, Hospital Admission Test, diseases and disorders, Technological Innovations, Technological Innovation, Transfer, Man, Routine Diagnostic, Hospital Admission, molecule, WMS, Routine Admission Tests, molecula, treatment, study, Biomarker, Transfer Learning, human disease, urinary levels, LCMSMS, molecules, Man (Taxonomy), Clinical, Diagnostic, peptides, Invention, Machine, gel, dysfunction, Biological Marker, Tissue, Innovation, Molekuel, Examination, Preadmission Physical Examination, non-neoplastic, OCTD, extruding from, Immunologic Markers, Immune, Markers, urinary aspects, Text, Routine, DmelCG1106, Viral Markers, disease management, Therapies, disorder, Homo sapiens disease, peptidos, Chromatographies, GPHYSD2, Immunologic Marker, Physical Examinations, Biologic, SGS, LC-MS2, Therapy, Innovations, Viral, Surrogate Endpoint, Immune Markers., RnBP, exits through, Modern, Proteins, Learning, Serum Markers, disorders, LC-MS/MS, Routine Admission, total expressed protein, GlcNAc 2-epimerase, End Point, Test, Biochemical Markers, Routine Diagnostic Test, medical condition, Mischung, Blood Serum, Hospital, Biologic Marker, Peptide, Immune Marker, ACMICD, Diagnostic Tests, Preadmission Physical Examinations, LC/MS/MS, N-acetyl-D-glucosamine 2-epimerase, Cytokine, Preadmission Physical, Marker, Surrogate End Point, Examinations, RENBP, Protein, Diseases, condition, MFS1, rare (European definition), WMS2, Biologic Markers, Epistemology, Serum Marker, distinct, End Points, Surrogate, Tests, Admission Tests, Endpoints, common, MASS, pathophysiology, Immunologic, exposed, Laboratory Marker, Treatments, human, Surrogate Marker, CG1106, AGE, loss of, Protein Gene Products, Diagnostic Test, Gene Proteins, disease, Therapeutic, Ion, Data, Biochemical Marker, liquid chromatography-tandem mass spectroscopy, Text Mining, Modern Man, SSKS, Admission Test, renin-binding protein, liquid chromatography tandem mass spectrometry, Treatment, Peptid, Polypeptide, Physical Examination, variable, cell bound, Proteomes, Serums, Technological, Routine Diagnostic TestsfalseUrine_appendicitisUrine proteomics for profiling of human disease, 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