Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods

Multidimensional separations combined with mass spectrometry are used to study the proteins that are present in two states of Drosophila melanogaster: the whole embryo and the adult head. The approach includes the incorporation of a gas-phase separation dimension in which ions are dispersed accordin...

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Bibliographic Details
Published in:Journal of proteome research 2005-07, Vol.4 (4), p.1223-1237
Main Authors: Taraszka, John A, Kurulugama, Ruwan, Sowell, Renã A, Valentine, Stephen J, Koeniger, Stormy L, Arnold, Randy J, Miller, David F, Kaufman, Thomas C, Clemmer, David E
Format: Article
Language:English
Subjects:
Animals
Calibration
Chromatography, Liquid - instrumentation
Chromatography, Liquid - methods
Databases, Nucleic Acid
Drosophila melanogaster - anatomy & histology
Drosophila melanogaster - embryology
Drosophila melanogaster - genetics
Drosophila melanogaster - metabolism
Genome
Insect Proteins - genetics
Insect Proteins - isolation & purification
Insect Proteins - metabolism
Mass Spectrometry - instrumentation
Mass Spectrometry - methods
Peptide Fragments - genetics
Peptide Fragments - metabolism
Proteome - analysis
Reproducibility of Results
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Summary:Multidimensional separations combined with mass spectrometry are used to study the proteins that are present in two states of Drosophila melanogaster: the whole embryo and the adult head. The approach includes the incorporation of a gas-phase separation dimension in which ions are dispersed according to differences in their mobilities and is described as a means of providing a detailed analytical map of the proteins that are present. Overall, we find evidence for 1133 unique proteins. In total, 780 are identified in the head, and 660 are identified in the embryo. Only 307 proteins are in common to both developmental stages, indicating that there are significant differences in these proteomes. A comparison of the proteome to a database of mRNAs that are found from analysis by cDNA approaches (i.e., transcriptome) also shows little overlap. All of this information is discussed in terms of the relationship between the predicted genome, and measured transcriptomes and proteomes. Additionally, the merits and weaknesses of current technologies are assessed in some detail.
ISSN:1535-3893
1535-3907
DOI:10.1021/pr050038g