title: Mapping the proteome of Drosophila melanogaster: analysis of embryos and adult heads by LC-IMS-MS methods.
abstract: 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.
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Taraszka
authors.forename: Ruwan
authors.initials: R
authors.lastname: Kurulugama
authors.forename: Renã A
authors.initials: RA
authors.lastname: Sowell
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Valentine
authors.forename: Stormy L
authors.initials: SL
authors.lastname: Koeniger
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Arnold
authors.forename: David F
authors.initials: DF
authors.lastname: Miller
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Kaufman
authors.forename: David E
authors.initials: DE
authors.lastname: Clemmer
mesh_terms: D000818:Animals; D002138:Calibration; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods*; D030561:Databases, Nucleic Acid; D004331:Drosophila melanogaster / Q000033:anatomy & histology / Q000196:embryology / Q000235:genetics / Q000378:metabolism; D016678:Genome; D019476:Insect Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D010446:Peptide Fragments / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results
chemical_list: D019476:Insect Proteins; D010446:Peptide Fragments; D020543:Proteome