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J Proteomics. 2014 Jan 31;97:62-8. doi: 10.1016/j.jprot.2013.06.020. Epub 2013 Jun 26.

A Candida albicans PeptideAtlas.

Author information

1
Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain. Electronic address: vvialasf@ucm.es.
2
Institute for Systems Biology, Seattle, WA, USA.
3
Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.
4
CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas, Spain.
5
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
6
Dept. Microbiología II, Universidad Complutense de Madrid, Madrid, Spain; IRYCIS: Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain. Electronic address: conchagil@ucm.es.

Abstract

Candida albicans public proteomic datasets, though growing steadily in the last few years, still have a very limited presence in online repositories. We report here the creation of a C. albicans PeptideAtlas comprising near 22,000 distinct peptides at a 0.24% False Discovery Rate (FDR) that account for over 2500 canonical proteins at a 1.2% FDR. Based on data from 16 experiments, we attained coverage of 41% of the C. albicans open reading frame sequences (ORFs) in the database used for the searches. This PeptideAtlas provides several useful features, including comprehensive protein and peptide-centered search capabilities and visualization tools that establish a solid basis for the study of basic biological mechanisms key to virulence and pathogenesis such as dimorphism, adherence, and apoptosis. Further, it is a valuable resource for the selection of candidate proteotypic peptides for targeted proteomic experiments via Selected Reaction Monitoring (SRM) or SWATH-MS.

BIOLOGICAL SIGNIFICANCE:

This C. albicans PeptideAtlas resolves the previous absence of fungal pathogens in the PeptideAtlas project. It represents the most extensive characterization of the proteome of this fungus that exists up to the current date, including evidence for uncharacterized ORFs. Through its web interface, PeptideAtlas supports the study of interesting proteins related to basic biological mechanisms key to virulence such as apoptosis, dimorphism and adherence. It also provides a valuable resource to select candidate proteotypic peptides for future (SRM) targeted proteomic experiments. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

KEYWORDS:

CGD; Candida Genome Database; Candida albicans; ESS; Empirical Suitability Score; FDR; False Discovery Rate; PRIDE; PSM; PSS; PeptideAtlas; Peptide–Spectrum Match; Predicted Suitability Score; Protein Identifications Database; Proteotypic peptides; SRM; Selected Reaction Monitoring

PMID:
23811049
PMCID:
PMC3951211
DOI:
10.1016/j.jprot.2013.06.020
[Indexed for MEDLINE]
Free PMC Article

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