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
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Dissertation
Approches protéomiques pour l’analyse des exosomes de liquides biologiques pour la recherche de biomarqueurs
TL;DR: Le dernier volet de cette these a ete consacre a l’analyse des exosomes du lavage broncho-alveolaire provenant de patients MV, maladie d’origine genetique qui atteint principalement les poumons.
Journal ArticleDOI
Proteomic Analysis of the Urine for Diagnostics in Newborns.
N. L. Starodubtseva,A. S. Kononikhin,Anna E. Bugrova,K. N. Krokhina,I. V. Nikitina,Yu. I. Kostyukevich,Igor Popov,Vladimir Frankevich,N. V. Aleksandrova,O. V. Ionov,Eugene N. Nikolaev,D.N. Degtyarev +11 more
TL;DR: Proteomic analysis of the urine was used for noninvasive diagnostics of abnormalities in newborns treated in the neonatal intensive care unit and can be used to differentiate between infectious and noninfectious respiratory disorders.
Protein biomarker-based screening for detection of recombinant bovine somatotropin abuse in dairy cows
TL;DR: Protein biomarker-based detection strategies are discussed against generic challenges in biomarker discovery and method development and biomarker analysis in serum and plasma samples from cattle, which are analysed using laboratory-based equipment.
Journal ArticleDOI
(Sugar-) Sweet Biomarkers? Clinical Proteomics Enters Sepsis Research.
Book ChapterDOI
Applications of peptide retention time in proteomic data analysis.
TL;DR: This chapter is a brief review of current methodologies of retention time prediction and application in proteomic analysis.
References
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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.