Journal ArticleDOI
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome.
Nagarjuna Nagaraj,Matthias Mann +1 more
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
A proteomic evaluation of urinary changes associated with cardiopulmonary bypass.
Ravi Kumar Dwivedi,Mario Navarrete,Nora Choi,Victor Spicer,Claudio Rigatto,Rakesh C. Arora,Oleg V. Krokhin,Julie Ho,John A. Wilkins +8 more
TL;DR: The results suggest that activation of the innate immune responses occur during cardiac bypass surgery, and the introduction of SWATH into the workflow offers a sample and instrument sparing approach to obtaining consistent in-depth sample analysis.
Journal ArticleDOI
Short Gel, Long Gradient Liquid Chromatography Tandem Mass Spectrometry to Discover Urinary Biomarkers of Chronic Pancreatitis.
TL;DR: Proteomic analysis of urine of chronic pancreatitis patients identified differentially abundant proteins in healthy controls and severe CP patients, which represent an initial set of targets for directed proteomics experiments for further validation studies.
Book ChapterDOI
Variations of Human Urinary Proteome
TL;DR: It can be known that the content of many urinary proteins maintain relatively stable, and there is reason to believe that the relatively stable urinary protein is a very valuable resource as biomarkers.
Journal ArticleDOI
A Quantitative Proteomic Analysis of Urine from Gamma-Irradiated Non-Human Primates
Stephanie D. Byrum,Marie Schluterman Burdine,Lisa M. Orr,Linley E. Moreland,Samuel G. Mackintosh,Simon Authier,Mylene Pouliot,Martin Hauer-Jensen,Alan J. Tackett +8 more
TL;DR: The proteomic study presented here is a comprehensive analysis of the urine proteome following radiation exposure and shows proteins involved in disease, cell adhesion, and metabolic pathway were significantly changed upon exposure to differing levels and durations of radiation exposure.
Journal ArticleDOI
Redox Proteomics in Study of Kidney-Associated Hypertension: New Insights to Old Diseases
TL;DR: Proteomics studies of kidney and related tissues have relevance to chronic kidney disease, and redox proteomics represents an under-exploited toolkit for identification of novel biomarkers in this commonly occurring pathology.
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.