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
Approaches to urinary detection of prostate cancer.
TL;DR: Conceptual and methodological advances in the field will help to drive the development of novel urinary tests that in turn may lead to a shift in the clinical paradigm for prostate cancer diagnosis and management.
Journal ArticleDOI
Alterations of the serum peptidome in renal cell carcinoma discriminating benign and malignant kidney tumors.
Erica Gianazza,Clizia Chinello,Veronica Mainini,Marta Cazzaniga,Valeria Squeo,Giancarlo Albo,Stefano Signorini,Salvatore S. Di Pierro,Stefano Ferrero,Simone Nicolardi,Yuri E. M. van der Burgt,André M. Deelder,Fulvio Magni +12 more
TL;DR: The results suggest the possibility to discriminate malignant kidney tumors based on a cluster of serum peptides and label-free approach may represent a valid method to verify results obtained by MALDI-TOF.
Journal ArticleDOI
Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma
Neil J. Shimwell,Richard T. Bryan,Wenbin Wei,Nicholas D. James,K K Cheng,Maurice P. Zeegers,Maurice P. Zeegers,Philip J. Johnson,Ashley Martin,Douglas G. Ward +9 more
TL;DR: Combined secretome-transcriptome analysis may be more useful than direct proteomic analysis of body fluids for biomarker discovery in both bladder cancer and other tumour types.
Journal ArticleDOI
Current trends in mass spectrometry of peptides and proteins: Application to veterinary and sports-doping control.
TL;DR: An overview of potential peptide and protein targets, including their amino acid sequence characteristics and current MS-based detection strategies is provided, and improvements of current and new detection strategies with state-of theart MS instrumentation are discussed for qualitative and quantitative approaches.
Journal ArticleDOI
The human proteome - A scientific opportunity for transforming diagnostics, therapeutics, and healthcare
Marc Vidal,Daniel W. Chan,Mark Gerstein,Matthias Mann,Gilbert S. Omenn,Danilo A. Tagle,Salvatore Sechi +6 more
TL;DR: The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics.
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.