ABSTRACT
Iron is essential and ubiquitous in living organisms. The competition for this micronutrient between the host and its pathogens has been related to disease establishment. Cryptococcus gattii is an encapsulated yeast that causes cryptococcosis mainly in immunocompetent individuals. In this study, we analyzed the proteomic profile of the C. gattii R265 Vancouver Island isolate under iron-depleted and -repleted conditions by multidimensional protein identification technology (MudPIT) and by 2D-GE. Proteins and key mechanisms affected by alteration of iron levels such as capsule production, cAMP-signaling pathway, response to stress, and metabolic pathways related to mitochondrial function were identified. Our results also show both proteomic methodologies employed to be complementary.
Subject(s)
Cryptococcus gattii/metabolism , Fungal Proteins/metabolism , Iron/physiology , Proteome/metabolism , Biosynthetic Pathways , Cryptococcus gattii/genetics , Cryptococcus gattii/growth & development , Electrophoresis, Gel, Two-Dimensional , Fungal Proteins/classification , Fungal Proteins/genetics , Gene Expression , Gene Expression Regulation, Fungal , Iron/metabolism , Molecular Sequence Annotation , Proteome/classification , Proteome/genetics , ProteomicsABSTRACT
SUMMARY: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (approximately 250%) and unique peptides (approximately 30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively. AVAILABILITY: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA CONTACT: paulo@pcarvalho.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Proteomics/methods , Software , Algorithms , Databases, FactualABSTRACT
UNLABELLED: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). We describe how YADA enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data. AVAILABILITY: http://fields.scripps.edu/yada