title: Reconstructed protein arrays from 3D HPLC/tandem mass spectrometry and 2D gels: complementary approaches to Porphyromonas gingivalis protein expression.
abstract: We compare typical qualitative protein identification data from two-dimensional (2D) polyacrylamide gel electrophoresis and reconstructed protein arrays, in the context of measuring protein expression by the Gram-negative periodontal pathogen Porphyromonas gingivalis. The arrays were assembled computationally from genome annotations and tandem mass spectrometry data from an off-line HPLC fractionation combined with 2D capillary HPLC analysis of whole proteome enzymatic digests. The 2D separation was carried out with a standard binary gradient HPLC system, modified only slightly with readily available components. Compared to 2D gels, the number of annotated open reading frames identified using the 3D HPLC approach was typically larger by at least a factor of 30. However, the newer technology is currently limited in its ability to reflect the many protein variants derived from posttranscriptional and posttranslational processing.
authors.affiliation: Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
authors.forename: Tiansong
authors.initials: T
authors.lastname: Wang
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Weibin
authors.initials: W
authors.lastname: Chen
authors.forename: Yoonsuk
authors.initials: Y
authors.lastname: Park
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Lamont
authors.forename: Murray
authors.initials: M
authors.lastname: Hackett
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis*; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional; D013058:Mass Spectrometry; D016966:Porphyromonas gingivalis / Q000737:chemistry*; D040081:Protein Array Analysis
chemical_list: D001426:Bacterial Proteins