Journal ArticleDOI
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome.
Nagarjuna Nagaraj,Matthias Mann +1 more
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
Proteomics Analysis of Urine to Examine Physical Effects of Warm Nano Mist Sauna Bathing.
Yoshitoshi Hirao,Naohiko Kinoshita,Naohiko Kinoshita,Bo Xu,Suguru Saito,Ali F. Quadery,Amr Elguoshy,Keiko Yamamoto,Tadashi Yamamoto +8 more
TL;DR: Proteomics analysis of urine samples obtained from healthy volunteers before and after they had taken a sauna bath with nano-mist or with conventional mist daily for two weeks indicated that considerable numbers of proteins were obviously up-regulated, with more than two-folds in urine samples after the nano-Mist sauna bathing.
Journal ArticleDOI
Urinary protein biomarkers based on LC–MS/MS analysis to discriminate vascular dementia from Alzheimer’s disease in Han Chinese population
TL;DR: In this article , the potential urine biomarkers of vascular dementia (VD) and unravel the diseaseassociated mechanisms by applying Liquid chromatography tandem-mass spectrometry (LC-MS/MS).
Patent
Compositions and methods for detecting Loa loa
TL;DR: In this article, methods of detecting the presence of Loa loa in a biological sample using one or more antigens, each having a different amino acid sequence selected from the group consisting of SEQ ID NOs: 1-20 Related compositions, specific binding partners, and test kits are also disclosed.
Journal ArticleDOI
Many kinds of oxidized proteins are present more in the urine of the elderly
TL;DR: In this paper , the authors explore differences in global chemical modifications of urinary protein at different ages, and show that the level of oxidized proteins in urine increased significantly with age and that oxidations are higher in older than younger ages.
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.