Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)

In the past decade, shotgun proteomic analysis has been utilized extensively to answer complex biological questions. New challenges arise in large scale proteomic profiling when dealing with complex biological mixtures such as the mammalian cell lysate. In this study, we explored the approach of pro...

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Bibliographic Details
Published in:Molecular & cellular proteomics 2006-01, Vol.5 (1), p.53-56
Main Authors: Chen, Emily I, Hewel, Johannes, Felding-Habermann, Brunhilde, Yates, 3rd, John R
Format: Article
Language:English
Subjects:
Biomarkers, Tumor - analysis
Biomarkers, Tumor - isolation & purification
Breast Neoplasms - chemistry
Breast Neoplasms - secondary
Chromatography, High Pressure Liquid
Chromatography, Ion Exchange
Electrophoresis, Gel, Two-Dimensional
Female
Humans
Isoelectric Focusing
Neoplasm Proteins - analysis
Neoplasm Proteins - isolation & purification
Proteomics - instrumentation
Proteomics - methods
Sequence Analysis, Protein
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Tumor Cells, Cultured
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Summary:In the past decade, shotgun proteomic analysis has been utilized extensively to answer complex biological questions. New challenges arise in large scale proteomic profiling when dealing with complex biological mixtures such as the mammalian cell lysate. In this study, we explored the approach of protein separation prior to the shotgun multidimensional protein identification technology (MudPIT) analysis. We fractionated the mammalian cancer cell lysate using the PF 2D ProteomeLab system and analyzed the distribution of molecular weight, isoelectric point, and cellular localization of the eluted proteins. As a result, we were able to reduce sample complexity by protein fractionation and increase the possibility of detecting proteins with lower abundance in the complex protein mixture.
ISSN:1535-9476
1535-9484
DOI:10.1074/mcp.T500013-MCP200