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
Citations
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Journal ArticleDOI
Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.
Yanbao Yu,Patricia Sikorski,Madeline Smith,Cynthia Bowman-Gholston,Nicolas Cacciabeve,Karen E. Nelson,Rembert Pieper +6 more
TL;DR: Network analysis supported the central role of neutrophil effector proteins in the defense against invading pathogens associated with subsequent coagulation and wound repair processes and should be useful as reference dataset in the search of biomarkers.
Journal ArticleDOI
Effect of Sweetened Dried Cranberry Consumption on Urinary Proteome and Fecal Microbiome in Healthy Human Subjects.
Nell A. Bekiares,Christian G. Krueger,Jennifer J. Meudt,Dhanansayan Shanmuganayagam,Jess D. Reed +4 more
TL;DR: Future larger clinical studies with multiomics and multitissue sampling designs are required to determine the effects of SDC consumption on nutrition and health.
Journal ArticleDOI
Profiling the proteome in renal transplantation
TL;DR: The current strategies used for proteomic‐based biomarker discovery in renal transplantation are described, inherent issues associated with these efforts are discussed and better strategies for successful biomarkers discovery are proposed.
Journal ArticleDOI
Identification of glycoproteins containing specific glycans using a lectin-chemical method.
Yan Li,Punit Shah,Angelo M. De Marzo,Jennifer E. Van Eyk,Qianqian Li,Daniel W. Chan,Hui Zhang +6 more
TL;DR: A novel method for rapid and quantitative identification of glycoproteins containing specific glycans by subsequent mass spectrometry is reported, which should be useful to facilitate the understanding of how changes in glycan associate with diseases, and to discover novel glycoprotein with certain glycans that could serve as biomarkers or therapeutic targets.
Journal ArticleDOI
An untargeted approach for the analysis of the urine peptidome of women with preeclampsia
Alexey S. Kononikhin,Alexey S. Kononikhin,N. L. Starodubtseva,N. L. Starodubtseva,Anna E. Bugrova,V.A. Shirokova,V V Chagovets,Maria I. Indeykina,Igor Popov,Yury Kostyukevich,O.V. Vavina,K.T. Muminova,Z.S. Khodzhaeva,N E Kan,V E Frankevich,Eugene N. Nikolaev,Eugene N. Nikolaev,Gennady T. Sukhikh +17 more
TL;DR: Analysis of the urine peptidome of women with PE revealed unique identifications that can potentially serve as early indicators of PE.
References
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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.