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The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins

BACKGROUND: Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our labo...

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Autores principales: Adachi, Jun, Kumar, Chanchal, Zhang, Yanling, Olsen, Jesper V, Mann, Matthias
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794545/
https://www.ncbi.nlm.nih.gov/pubmed/16948836
http://dx.doi.org/10.1186/gb-2006-7-9-r80
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author Adachi, Jun
Kumar, Chanchal
Zhang, Yanling
Olsen, Jesper V
Mann, Matthias
author_facet Adachi, Jun
Kumar, Chanchal
Zhang, Yanling
Olsen, Jesper V
Mann, Matthias
author_sort Adachi, Jun
collection PubMed
description BACKGROUND: Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our laboratory has developed methods for the in-depth characterization of body fluids; these involve a linear ion trap-Fourier transform (LTQ-FT) and a linear ion trap-orbitrap (LTQ-Orbitrap) mass spectrometer. Here we applied these methods to the analysis of the human urinary proteome. RESULTS: We employed one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis and reverse phase high-performance liquid chromatography for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution, and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at parts per million accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in urine obtained from ten healthy donors, while essentially eliminating false-positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene Ontology (GO) analysis. Furthermore, extracellular, lysosomal, and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are probably present in urine by secretion in exosomes. CONCLUSION: Our analysis provides a high-confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained using different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future.
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spelling pubmed-17945452007-02-08 The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins Adachi, Jun Kumar, Chanchal Zhang, Yanling Olsen, Jesper V Mann, Matthias Genome Biol Research BACKGROUND: Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our laboratory has developed methods for the in-depth characterization of body fluids; these involve a linear ion trap-Fourier transform (LTQ-FT) and a linear ion trap-orbitrap (LTQ-Orbitrap) mass spectrometer. Here we applied these methods to the analysis of the human urinary proteome. RESULTS: We employed one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis and reverse phase high-performance liquid chromatography for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution, and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at parts per million accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in urine obtained from ten healthy donors, while essentially eliminating false-positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene Ontology (GO) analysis. Furthermore, extracellular, lysosomal, and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are probably present in urine by secretion in exosomes. CONCLUSION: Our analysis provides a high-confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained using different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future. BioMed Central 2006 2006-09-01 /pmc/articles/PMC1794545/ /pubmed/16948836 http://dx.doi.org/10.1186/gb-2006-7-9-r80 Text en Copyright © 2006 Adachi et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Adachi, Jun
Kumar, Chanchal
Zhang, Yanling
Olsen, Jesper V
Mann, Matthias
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title_full The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title_fullStr The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title_full_unstemmed The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title_short The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
title_sort human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794545/
https://www.ncbi.nlm.nih.gov/pubmed/16948836
http://dx.doi.org/10.1186/gb-2006-7-9-r80
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