A Candida albicans PeptideAtlas

Vialás, Vital; Sun, Zhi; Penha, Carla V. Loureiro y; Carrascal, Montserrat; Abián, Joaquín; Monteoliva, Lucía; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Gil, Concha

doi:10.1016/j.jprot.2013.06.020

Cited by 20 publications

(17 citation statements)

References 42 publications

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“…The data corresponded to three biological replicates for yeast samples and four biological replicates for hyphal samples. They are deposited in the PeptideAtlas database [47], and information on each protein can be accessed through the CGD.…”

Section: Resultsmentioning

confidence: 99%

Candida albicans cell shaving uncovers new proteins involved in cell wall integrity, yeast to hypha transition, stress response and host–pathogen interaction

Gil-Bona

Parra-Giraldo

Hernáez

et al. 2015

Journal of Proteomics

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The ability to switch from yeast to hyphal growth is essential for virulence in Candida albicans. The cell surface is the initial point of contact between the fungus and the host. In this work, a free-gel proteomic strategy based on tryptic digestion of live yeast and hyphae cells and protein identification using LC-MS/MS methodology was used to identify cell surface proteins. Using this strategy, a total of 943 proteins were identified, of which 438 were in yeast and 928 were in hyphae. Of these proteins, 79 were closely related to the organization and biogenesis of the cell wall, including 28 GPI-anchored proteins, such as Hyr1 and Sod5 which were detected exclusively in hyphae, and Als2 and Sap10which were detected only in yeast. A group of 17 proteins of unknown function were subsequently studied by analysis of the corresponding deletion mutants. We found that four new proteins, Pst3, Tos1, Orf19.3060 and Orf19.5352 are involved in cell wall integrity and in C. albicans’ engulfment by macrophages. Moreover, the putative NADH-ubiquinone-related proteins, Ali1, Mci4, Orf19.287 and Orf19.7590, are also involved in osmotic and oxidative resistance, yeast to hypha transition and the ability to damage and invade oral epithelial cells.

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Section: Resultsmentioning

confidence: 99%

Candida albicans cell shaving uncovers new proteins involved in cell wall integrity, yeast to hypha transition, stress response and host–pathogen interaction

Gil-Bona

Parra-Giraldo

Hernáez

et al. 2015

Journal of Proteomics

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“…However, despite the extensive efforts on clinical aspects from the proteomics view [9-12], online public proteomic repositories were sparse. Our previously published C. albicans PeptideAtlas [13] described the first large-scale public proteomic resource for the study of this opportunistic pathogenic fungus. With over 2500 proteins and representing approximately 41% of the predicted proteome, the C. albicans PeptideAtlas attained unprecedented proteome coverage and is still the first human fungal pathogen present in the PeptideAtlas project [14,15].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, two high-resolution C. albicans MS datasets corresponding to published works on the secreted proteome [20] and on the yeast and hyphal cell forms surface proteome [21] have also been included in the compilation of MS data files. These new datasets, along with the previously stored raw MS datafiles comprising the former version of the C. albicans PeptideAtlas [13], have all been reprocessed and analyzed through the Trans Proteomics Pipeline, TPP [22,23] using multi-search search engine approach utilizing a sequence database with allele-specific sequences to generate the most comprehensive existing C. albicans proteomics resource with unprecedented proteome coverage.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage

Vialás

Sun

Reales-Calderón

et al. 2016

Journal of Proteomics

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To provide new and expanded proteome documentation of the opportunistically pathogen Candida albicans, we have developed new protein extraction and analysis routines to provide a new, extended and enhanced version of the C. albicans PeptideAtlas. Two new datasets, resulting from experiments consisting of exhaustive subcellular fractionations and different growing conditions, plus two additional datasets from previous experiments on the surface and the secreted proteomes, have been incorporated to increase the coverage of the proteome. High resolution precursor mass spectrometry (MS) and ion trap tandem MS spectra were analyzed with three different search engines using a database containing allele-specific sequences. This approach, novel for a large-scale C. albicans proteomics project, was combined with the post-processing and filtering implemented in the Trans Proteomic Pipeline consistently used in the PeptideAtlas project and resulted in 49372 additional peptides (3-fold increase) and 1630 more proteins (1.6-fold increase) identified in the new C. albicans PeptideAtlas with respect to the previous build. A total of 71310 peptides and 4174 canonical (minimal non-redundant set) proteins (4115 if one protein per pair of alleles is considered) were identified representing 66% of the 6218 proteins in the predicted proteome. This makes the new PeptideAtlas build the most comprehensive C. albicans proteomics resource available and the only large-scale one with detections of individual alleles.

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“…Last year’s PeptideAtlas update for the Journal of Proteome Research 2 nd C-HPP special issue focused on a comparison between three sample subtypes, kidney, urine, and blood plasma 7 . In addition to human builds, there are PeptideAtlas builds for many other important species, including recent new builds for cow 8 , horse 9 , and C. albicans 10 . A key focus of the PeptideAtlas is maintaining a well-understood and carefully controlled false discovery rate (FDR) for the identifications contained therein.…”

Section: Introductionmentioning

confidence: 99%

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet

et al. 2015

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The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different labs, all reanalyzed through a uniform processing pipeline. The latest 2015-03 build contains substantially more input data than past releases, is mapped to a recent version of our merged reference proteome, and uses improved informatics processing and the development of the AtlasProphet to provide the highest quality results. Within the set of ~20,000 neXtProt primary entries, 14,070 (70%) are confidently detected in the latest build, 5% are ambiguous, 9% are redundant, leaving the total percentage of proteins for which there are no mapping detections at just 16% (3166), all derived from over 133 million peptide-spectrum matches identifying more than 1 million distinct peptides using AtlasProphet to characterize and classify the protein matches. Improved handling for detection and presentation of single amino-acid variants (SAAVs) reveals the detection of 5,326 uniquely mapping SAAVs across 2,794 proteins. With such a large amount of data, the control of false positives is a challenge. We present the methodology and results for maintaining rigorous quality, along with a discussion of the implications of the remaining sources of errors in the build. We check our uncertainty estimates against a set of olfactory receptor proteins not expected to be present in the set. We show how the use of synthetic reference spectra can provide confirmatory evidence for claims of detection of proteins with weak evidence.

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A Candida albicans PeptideAtlas

Cited by 20 publications

References 42 publications

Candida albicans cell shaving uncovers new proteins involved in cell wall integrity, yeast to hypha transition, stress response and host–pathogen interaction

Candida albicans cell shaving uncovers new proteins involved in cell wall integrity, yeast to hypha transition, stress response and host–pathogen interaction

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet

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