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.