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
Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments.
Evelyne Maes,Dirk Valkenborg,Geert Baggerman,Hanny Willems,Bart Landuyt,Liliane Schoofs,Inge Mertens +6 more
TL;DR: It is illustrated that the variability induced by TMT labeling is small when compared to the technical variation, and the latter is also responsible for a substantial part of the total variation.
Journal ArticleDOI
An individual urinary proteome analysis in normal human beings to define the minimal sample number to represent the normal urinary proteome
TL;DR: The minimum sample number is 10 and requires a balanced number of males and females in order to obtain a representative normal human urinary proteome and the variation of protein abundance was defined and the minimal sample number for quantitative proteomic analysis was identified.
Journal ArticleDOI
Platelet Releasate Proteome Profiling Reveals a Core Set of Proteins with Low Variance between Healthy Adults.
Martin Parsons,Martin Parsons,Paulina B. Szklanna,Paulina B. Szklanna,Jose A. Guerrero,Kieran Wynne,Feidhlim Dervin,Karen O'Connell,Seamus Allen,Karl Egan,Karl Egan,Cavan Bennett,Christopher McGuigan,Cedric Gheveart,Fionnuala Ní Áinle,Patricia B. Maguire +15 more
TL;DR: Taken together, the PR contains valuable soluble and vesicular cargo and has low‐population variance among healthy adults, rendering it a potentially useful platform for diagnostic fingerprinting of platelet‐related disease.
Journal ArticleDOI
The tissue proteome in the multi-omic landscape of kidney disease.
TL;DR: The authors discuss proteomics research findings in nephrology and the potential, as well as the limitations, of using proteomics techniques to uncover disease mechanisms and develop new therapeutic strategies.
Journal ArticleDOI
Identification of biological markers for better characterization of older subjects with physical frailty and sarcopenia
TL;DR: Possible biological markers to be considered in the framing of physical frailty and sarcopenia are indicated and discussed.
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.
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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
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