Supporting data for analysis of the Helicobacter pylori exoproteome

Abstract

The goal of this research was to analyze the composition of the Helicobacter pylori exoproteome at multiple phases of bacterial growth (Snider et al., 2015) [1]. H. pylori was grown in a serum-free medium and at serial time points, aliquots were centrifuged and fractionated to yield culture supernatant, a soluble cellular fraction, and a membrane fraction. Samples were analyzed by single dimensional LC-MS/MS analyses and multidimensional protein identification technology (MudPIT). Here we present data showing the numbers of assigned spectra and proportional abundance of individual proteins in each of the samples analyzed, along with a calculation of the level of enrichment of individual proteins in the supernatant compared to the soluble cellular fraction.

Growth phase-dependent composition of the Helicobacter pylori exoproteome

“…In total, we identified 74 proteins that were enriched in the culture supernatant at two or more time points (19). Twenty-five of these proteins were significantly enriched in the supernatant at ≥4 time points (Table 1).…”

“…Specifically, we investigated the relative abundance of proteins in the soluble (CP/PP) and membrane fractions, and thereby determined whether individual proteins were localized predominantly to a soluble bacterial fraction (corresponding to cytoplasmic or periplasmic localization) or a membrane-associated bacterial fraction. Many of the selectively released proteins (including several annotated as “conserved hypothetical secreted proteins”) were localized mainly to a soluble bacterial fraction, and we speculate that these proteins are released directly from the cytoplasm or periplasm into the extracellular space (Table 1 and (19)). Other putative secreted proteins, including VacA, were localized mainly to a membrane-associated bacterial fraction.…”

“…To facilitate further analysis, the levels of enrichment were expressed as log 2 values (log 2 E sup ). To analyze the results of 1D mass spectrometric analyses, the data from three independent experiments were merged (19). E sup , Fisher’s exact test, Bonferroni multiple test corrections, and construction of Venn diagrams were performed in R (http://www.R-project.org).…”

Future of Urological Diagnosis Using Proteomics: A Review of Literature

“…This review article in particular focuses on the impact of proteomics in the field of urology. Sodium Dodecyl Sulfate-PolyAcrylamide Gel Electrophoresis [8] Two-Dimensional-Differential In-Gel Electrophoresis [8] Multi-Dimensional Protein Identification Technology [9][10][11] Ultracentrifugation [12] Table 2 Technologies used for proteomics: Protein identification.…”