Journal ArticleDOI
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome.
Nagarjuna Nagaraj,Matthias Mann +1 more
Reads0
Chats0
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
Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack
TL;DR: Current methods for target identification of small molecules are summarized, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound.
Journal ArticleDOI
High-sensitivity Analytical Approaches for the Structural Characterization of Glycoproteins
TL;DR: The focus of the review has been on glycoanalytical chemistry, which aims to isolate and structurally characterize biologically important glycoconjugates and synthesize carbohydrate structures for biochemical investigations, enabling technologies and medical applications and providing new therapeutics.
Journal ArticleDOI
A comprehensive map of the human urinary proteome.
Arivusudar Marimuthu,Robert N. O'Meally,Raghothama Chaerkady,Yashwanth Subbannayya,Vishalakshi Nanjappa,Praveen Kumar,Dhanashree S. Kelkar,Sneha M. Pinto,Rakesh Sharma,Santosh Renuse,Renu Goel,Rita Christopher,Bernard Delanghe,Robert N. Cole,H. C. Harsha,Akhilesh Pandey +15 more
TL;DR: A comprehensive analysis of human urinary proteome from healthy individuals using high-resolution Fourier transform mass spectrometry identified 1,823 proteins, of which 671 proteins have not previously been reported as constituents of human urine.
Journal ArticleDOI
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
Niklas Grassl,Nils A. Kulak,Garwin Pichler,Philipp E. Geyer,Philipp E. Geyer,Jette Jung,Soeren Schubert,Pavel Sinitcyn,Juergen Cox,Matthias Mann,Matthias Mann +10 more
TL;DR: Rapid shotgun and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies.
Journal ArticleDOI
Sources of Technical Variability in Quantitative LC–MS Proteomics: Human Brain Tissue Sample Analysis
Paul D. Piehowski,Vladislav A. Petyuk,Daniel J. Orton,Fang Xie,Ronald J. Moore,Manuel Ramirez-Restrepo,Anzhelika Engel,Andrew P. Lieberman,Roger L. Albin,David G. Camp,Richard D. Smith,Amanda J. Myers +11 more
TL;DR: An experimental strategy that allows for a detailed examination of the variability of the quantitative LC-MS proteomics measurements is presented and the stability of the platform and its suitability for discovery proteomics studies is demonstrated.
References
More filters
Journal ArticleDOI
Identification and proteomic profiling of exosomes in human urine
TL;DR: The results indicate that exosome isolation may provide an efficient first step in biomarker discovery in urine and identify numerous protein components of MVBs and of the endosomal pathway in general.
Journal ArticleDOI
Genesis: cluster analysis of microarray data
TL;DR: Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.
Journal ArticleDOI
Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap
Jesper V. Olsen,Jesper V. Olsen,Lyris M. F. de Godoy,Guoqing Li,Guoqing Li,Boris Macek,Peter Mortensen,Reinhold Pesch,Alexander Makarov,Oliver Lange,Stevan Horning,Matthias Mann,Matthias Mann +12 more
TL;DR: This work demonstrates sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap to the orbitrap mass spectrometer (LTQ Orbitrap), and introduces a variable mass tolerance to improve certainty of peptide and small molecule identification.
Journal ArticleDOI
Microarray data analysis: from disarray to consolidation and consensus.
TL;DR: In just a few years, microarrays have gone from obscurity to being almost ubiquitous in biological research, and points of consensus are emerging about the general approaches that warrant use and elaboration.
Journal ArticleDOI
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.
Lyris M. F. de Godoy,Jesper V. Olsen,Jürgen Cox,Michael L. Nielsen,Nina C. Hubner,Florian Fröhlich,Tobias C. Walther,Matthias Mann +7 more
TL;DR: Comparison of protein levels of essentially all endogenous proteins in haploid yeast cells to their diploid counterparts spans more than four orders of magnitude in protein abundance with no discrimination against membrane or low level regulatory proteins.