Table of Contents
International Journal of Proteomics
Volume 2013, Article ID 279590, 10 pages
Research Article

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans

1Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999/MS K8-98, Richland, WA 99352, USA
2Center for Bioproducts and Bioenergy, Washington State University, Richland, WA, USA
3Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
4Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA, USA
5Department of Neurobiology, 720 Westview Drive SW, Atlanta, GA, USA

Received 7 October 2012; Revised 31 January 2013; Accepted 4 February 2013

Academic Editor: Boris Zybailov

Copyright © 2013 Si Wu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome of Novosphingobium aromaticivorans. Our top-down analysis provided the confident identification of 55 proteins in the periplasm and characterized their PTMs including signal peptide removal, N-terminal methionine excision, acetylation, glutathionylation, pyroglutamate, and disulfide bond formation. This study provides the first experimental evidence for the expression and periplasmic localization of many hypothetical and uncharacterized proteins and the first unrestrictive, large-scale data on PTMs in the bacterial periplasm.