Development of a Targeted Urine Proteome Assay for kidney diseases

Since human urine is the most readily available biofluid whose proteome changes in response to disease, it is a logical sample for identifying protein biomarkers for kidney diseases.

[1]  Lisa M. Chung,et al.  Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins , 2015, Proteomics.

[2]  A. Nairn,et al.  YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research , 2015, Genom. Proteom. Bioinform..

[3]  B. Knebelmann,et al.  A new workflow for proteomic analysis of urinary exosomes and assessment in cystinuria patients. , 2015, Journal of proteome research.

[4]  Jesper V Olsen,et al.  Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer. , 2014, Journal of proteome research.

[5]  J. Yates,et al.  Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics , 2014, Journal of proteome research.

[6]  Darryl B. Hardie,et al.  Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. , 2014, Biochimica et biophysica acta.

[7]  F. Frey,et al.  Identification of IGFBP-7 by urinary proteomics as a novel prognostic marker in early acute kidney injury. , 2014, Kidney international.

[8]  Susan E. Abbatiello,et al.  Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach* , 2014, Molecular & Cellular Proteomics.

[9]  Pei Wang,et al.  Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins , 2013, Nature Methods.

[10]  M. Senko,et al.  Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. , 2013, Analytical chemistry.

[11]  Christoph H Borchers,et al.  Multiplexed MRM‐based quantitation of candidate cancer biomarker proteins in undepleted and non‐enriched human plasma , 2013, Proteomics.

[12]  J. Yates,et al.  Digestion and depletion of abundant proteins improves proteomic coverage , 2013, Nature Methods.

[13]  Ruedi Aebersold,et al.  Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics , 2012, Science Translational Medicine.

[14]  Juncong Yang,et al.  MRM‐based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma , 2012, Proteomics.

[15]  M. Perazella,et al.  Risk of poor outcomes with novel and traditional biomarkers at clinical AKI diagnosis. , 2011, Clinical journal of the American Society of Nephrology : CJASN.

[16]  S. Carr,et al.  A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease , 2011, Nature Biotechnology.

[17]  Pei Wang,et al.  A targeted proteomics–based pipeline for verification of biomarkers in plasma , 2011, Nature Biotechnology.

[18]  M. Mann,et al.  Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome. , 2011, Journal of proteome research.

[19]  P. Righetti,et al.  The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries , 2010, Expert review of proteomics.

[20]  Christoph H Borchers,et al.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma , 2009, Nature Biotechnology.

[21]  A. Dominiczak,et al.  CE‐MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics , 2008, Proteomics. Clinical applications.

[22]  Henry H. N. Lam,et al.  PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.

[23]  H. Christofk,et al.  A label‐free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen , 2008, Proteomics.

[24]  Kei-Hoi Cheung,et al.  YPED: a web-accessible database system for protein expression analysis. , 2007, Journal of proteome research.

[25]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[26]  M. Mann,et al.  The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins , 2006, Genome Biology.

[27]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[28]  L. Leuthold,et al.  Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. , 2004, Journal of mass spectrometry : JMS.

[29]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[30]  M. Ünlü,et al.  Difference gel electrophoresis. A single gel method for detecting changes in protein extracts , 1997, Electrophoresis.