Journal ArticleDOI
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome.
Nagarjuna Nagaraj,Matthias Mann +1 more
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TLDR
Determination of the normal fluctuation of individual urinary proteins should be useful in establishing significance thresholds in biomarker studies and allowed definition of a common and abundant set of 500 proteins that were readily detectable in all studied individuals.Abstract:
Urine is a readily and noninvasively obtainable body fluid. Mass spectrometry (MS)-based proteomics has shown that urine contains thousands of proteins. Urine is a potential source of biomarkers for diseases of proximal and distal tissues but it is thought to be more variable than the more commonly used plasma. By LC-MS/MS analysis on an LTQ-Orbitrap without prefractionation we characterized the urinary proteome of seven normal human donors over three consecutive days. Label-free quantification of triplicate single runs covered the urinary proteome to a depth of more than 600 proteins. The median coefficient of variation (cv) of technical replicates was 0.18. Interday variability was markedly higher with a cv of 0.48 and the overall variation of the urinary proteome between individuals was 0.66. Thus technical variability in our data was 7.5%, whereas intrapersonal variability contributed 45.5% and interpersonal variability contributed 47.1% to total variability. Determination of the normal fluctuation of individual urinary proteins should be useful in establishing significance thresholds in biomarker studies. Our data also allowed definition of a common and abundant set of 500 proteins that were readily detectable in all studied individuals. This core urinary proteome has a high proportion of secreted, membrane, and relatively high-molecular weight proteins.read more
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Journal ArticleDOI
Proteome Profiling of Diabetic Mellitus Patient Urine for Discovery of Biomarkers by Comprehensive MS-Based Proteomics.
Yoshitoshi Hirao,Suguru Saito,Hidehiko Fujinaka,Shigeru Miyazaki,Bo Xu,Ali F. Quadery,Amr Elguoshy,Keiko Yamamoto,Tadashi Yamamoto +8 more
TL;DR: Complete proteomics analysis of urine proteomes of diabetic mellitus patients without microalbuminuria and healthy volunteers is performed to compare the protein profiles by mass spectrometry and the discovery of a useful biomarker for early DN discovery is expected.
Journal ArticleDOI
Label-free study of cosmonaut's urinary proteome changes after long-duration spaceflights.
A. G. Brzhozovskiy,A. S. Kononikhin,A. S. Kononikhin,Maria I. Indeykina,LKh Pastushkova,Igor Popov,E. N. Nikolaev,E. N. Nikolaev,Irina M. Larina +8 more
TL;DR: The proteomic analysis of cosmonauts’ urine samples provides new data on the human body’s adaptation to ground conditions after long-duration spaceflight, and identifies proteins related with stress and response to stimulus.
Journal ArticleDOI
Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems
Chiara Ilgrande,Tom Defoirdt,Siegfried E. Vlaeminck,Siegfried E. Vlaeminck,Nico Boon,Peter Clauwaert +5 more
TL;DR: Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.
Journal ArticleDOI
Unveiling the rat urinary proteome with three complementary proteomics approaches
Fernando Sánchez-Juanes,María Del Carmen Muñiz,César Raposo,Silvia Rodríguez-Prieto,Alberto Paradela,Yaremi Quiros,Francisco J. López-Hernández,José Manuel González-Buitrago,Laura Ferreira +8 more
TL;DR: The analysis affords the most extensive rat urinary protein database currently available and this may be useful in the study of renal physiology and in the search for biomarkers related to renal and nonrenal diseases.
Journal ArticleDOI
Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort
Yanbao Yu,Harinder Singh,Keehwan Kwon,Tamara Tsitrin,Joann Petrini,Karen E. Nelson,Rembert Pieper +6 more
TL;DR: Quantitative analysis of proinflammatory cytokines in blood plasma and more than 500 proteins in urine identified the regulation of coagulation, antimicrobial humoral immune responses, and the IL-12 signaling pathway as enriched GO terms.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more
TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
Journal ArticleDOI
Mass spectrometry-based proteomics
Ruedi Aebersold,Matthias Mann +1 more
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Journal ArticleDOI
Universal sample preparation method for proteome analysis
TL;DR: A method is described, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics and allows single-run analyses of organelles and an unprecedented depth of proteome coverage.
Journal ArticleDOI
Stop and Go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and lc/ms sample pretreatment in proteomics
TL;DR: A novel procedure in which a very small disk of beads embedded in a Teflon meshwork is placed as a microcolumn into pipet tips, finding that the Stage system is well-suited as a universal sample preparation system for proteomics.