In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics

Jun Adachi, Chanchal Kumar, Yanling Zhang, Matthias Mann

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Udgivelsesdato: 2007-Jul
OriginalsprogEngelsk
TidsskriftMolecular and Cellular Proteomics
Vol/bind6
Udgave nummer7
Sider (fra-til)1257-1273
Antal sider16
ISSN1535-9476
DOI
StatusUdgivet - 1. jul. 2007

Fingeraftryk

Proteome
Bioinformatics
Computational Biology
Adipocytes
Mass spectrometry
Proteins
Insulin
Mitochondria
Microarrays
Fractionation
Cytosol
Energy Metabolism
Genes
Membranes
Messenger RNA
Databases
Chemical analysis
Proteomics

Citer dette

Adachi, Jun ; Kumar, Chanchal ; Zhang, Yanling ; Mann, Matthias. / In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics. I: Molecular and Cellular Proteomics. 2007 ; Bind 6, Nr. 7. s. 1257-1273.
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title = "In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics",
abstract = "Adipocytes are central players in energy metabolism and the obesity epidemic, yet their protein composition remains largely unexplored. We investigated the adipocyte proteome by combining high accuracy, high sensitivity protein identification technology with subcellular fractionation of nuclei, mitochondria, membrane, and cytosol of 3T3-L1 adipocytes. We identified 3,287 proteins while essentially eliminating false positives, making this one of the largest high confidence proteomes reported to date. Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized role, is very complex. Comparison with microarray data showed that the mRNA abundance of detected versus non-detected proteins differed by less than 2-fold and that proteomics covered as large a proportion of the insulin signaling pathway. We used the Endeavour gene prioritization algorithm to associate a number of factors with vesicle transport in response to insulin stimulation, a key function of adipocytes. Our data and analysis can serve as a model for cellular proteomics. The adipocyte proteome is available as supplemental material and from the Max-Planck Unified Proteome database.",
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In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics. / Adachi, Jun; Kumar, Chanchal; Zhang, Yanling; Mann, Matthias.

I: Molecular and Cellular Proteomics, Bind 6, Nr. 7, 01.07.2007, s. 1257-1273.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

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AU - Adachi, Jun

AU - Kumar, Chanchal

AU - Zhang, Yanling

AU - Mann, Matthias

PY - 2007/7/1

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N2 - Adipocytes are central players in energy metabolism and the obesity epidemic, yet their protein composition remains largely unexplored. We investigated the adipocyte proteome by combining high accuracy, high sensitivity protein identification technology with subcellular fractionation of nuclei, mitochondria, membrane, and cytosol of 3T3-L1 adipocytes. We identified 3,287 proteins while essentially eliminating false positives, making this one of the largest high confidence proteomes reported to date. Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized role, is very complex. Comparison with microarray data showed that the mRNA abundance of detected versus non-detected proteins differed by less than 2-fold and that proteomics covered as large a proportion of the insulin signaling pathway. We used the Endeavour gene prioritization algorithm to associate a number of factors with vesicle transport in response to insulin stimulation, a key function of adipocytes. Our data and analysis can serve as a model for cellular proteomics. The adipocyte proteome is available as supplemental material and from the Max-Planck Unified Proteome database.

AB - Adipocytes are central players in energy metabolism and the obesity epidemic, yet their protein composition remains largely unexplored. We investigated the adipocyte proteome by combining high accuracy, high sensitivity protein identification technology with subcellular fractionation of nuclei, mitochondria, membrane, and cytosol of 3T3-L1 adipocytes. We identified 3,287 proteins while essentially eliminating false positives, making this one of the largest high confidence proteomes reported to date. Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized role, is very complex. Comparison with microarray data showed that the mRNA abundance of detected versus non-detected proteins differed by less than 2-fold and that proteomics covered as large a proportion of the insulin signaling pathway. We used the Endeavour gene prioritization algorithm to associate a number of factors with vesicle transport in response to insulin stimulation, a key function of adipocytes. Our data and analysis can serve as a model for cellular proteomics. The adipocyte proteome is available as supplemental material and from the Max-Planck Unified Proteome database.

KW - 3T3-L1 Cells

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KW - Animals

KW - Cell Fractionation

KW - Computational Biology

KW - Humans

KW - Mice

KW - Oligonucleotide Array Sequence Analysis

KW - Organelles

KW - Proteasome Endopeptidase Complex

KW - Proteome

KW - RNA, Messenger

KW - Ribosomes

KW - Signal Transduction

KW - Tandem Mass Spectrometry

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DO - 10.1074/mcp.M600476-MCP200

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JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

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