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
Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome.
Nico Jehmlich,K. H. D. Dinh,Manuela Gesell-Salazar,Elke Hammer,Leif Steil,Vishnu M. Dhople,Claudia Schurmann,Birte Holtfreter,Thomas Kocher,Uwe Völker +9 more
TL;DR: 2-D DIGE as well as LC-MS/MS approaches are suitable for biomarker screening in saliva and should thus be used as complementary approaches.
Journal ArticleDOI
A new workflow for proteomic analysis of urinary exosomes and assessment in cystinuria patients.
Matthieu Bourderioux,Thao Nguyen-Khoa,Cerina Chhuon,Ludovic Jeanson,Danielle Tondelier,Marta Walczak,Mario Ollero,Soumeya Bekri,Bertrand Knebelmann,Estelle Escudier,Bernard Escudier,Aleksander Edelman,Ida Chiara Guerrera +12 more
TL;DR: This is the first successful proteomic study in cystinuria unmasking the potential role of inflammation in this disease, and the workflow developed is applicable to investigate urinary exosomes in different renal diseases and to search for diagnostic/prognostic markers.
Journal ArticleDOI
Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences.
Chen Shao,Chen Shao,Mindi Zhao,Xizhao Chen,Haidan Sun,Yehong Yang,Xiaoping Xiao,Xiaoping Xiao,Zhengguang Guo,Xiaoyan Liu,Yang Lv,Xiangmei Chen,Wei Sun,Di Wu,Youhe Gao +14 more
TL;DR: It is suggested that future biomarker investigations should consider gender as a crucial factor in experimental design and data analysis and reference intervals of proteins as the baseline for biomarker discovery.
Journal ArticleDOI
Categorizing Biomarkers of the Human Exposome and Developing Metrics for Assessing Environmental Sustainability
TL;DR: The philosophy of long-term environmental sustainability is explored in the context of human biomarker measurements and how empirical data can be collected and interpreted to assess if solutions to existing environmental problems might have unintended consequences.
Journal ArticleDOI
Searching for New Biomarkers of Renal Diseases through Proteomics
TL;DR: It is clear that the field of proteomics has not yet fulfilled its promise, but ongoing efforts to standardize sample collection and preparation, improve study designs, perform multicenter validations, and create joint industry-regulatory bodies offer promise for the recognition of novel molecules that could change clinical nephrology forever.
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.