{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-3007x1F-2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-3007x1F-4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB1-7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-WT2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-3007x1F-3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-3007x1F-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-WT3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-WT1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/July272023-BB6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/Dec2422-BB-WT4.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/search-EV.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD051506/search-COIP.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["jgeddesm@uoguelph.ca"],"submitter":["Jennifer Geddes-McAlister"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Cryptococcosis"],"software":[""],"submitter_keywords":["Infection","Immunization","Quantitative proteomics","Virulence","Drug discovery","Phenome","Fungal pathogenesis"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD051506"],"tissue":["Cell Culture","Extracellular Membrane-bounded Organelle","Defense Response To Fungus","Macrophage"],"sample_protocol":["PBS-washed cell pellets (fungal and macrophage) were resuspended in 100 mM Tris-HCl (pH 8.5) with a protease inhibitor cocktail tablet (PIC; Sigma-Aldrich), followed by probe sonication (Thermo Fisher Scientific) in an ice bath. Sodium dodecyl sulfate (SDS) (2% final) was added, followed by reduction with 10 mM dithiothreitol (DTT) at 95 ˚C for 10 min with 800 rpm. Next, alkylation was performed with 55 mM iodoacetamide (IAA) at room temperature in the dark, and acetone precipitation (80% final) overnight at -20 ˚C. Samples were collected and washed twice in 80% acetone, dried, and resuspended in 8 M urea-40 mM HEPES for protein quantification using bovine serum albumin (BSA) tryptophan assay. Samples were diluted to 2 M urea with 50 mM ammonium bicarbonate (ABC), normalized to 100 µg protein, and digested with LysC-trypsin (Promega [protein/enzyme ratio, 50:1]). For secretome samples, the fungal-YPD supernatant was filtered (0.22 µm syringe filter tip), reduced with 10 mM DTT (30 min, room temperature), alkylated with 55 mM IAA (20 min, in the dark), and digested with LysC-trypsin overnight as described above. Digestion was stopped with 10% (v/v) trifluoracetic acid (TFA), and acidified peptides were purified using Stop-And-Go extraction tips (Stage tips; containing three layers of C18 ) to desalt and purify following standard instructions.  Peptides were initially resuspended in Buffer A (2% acetonitrile [ACN], 0.1% TFA) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Peptides were subjected to nanoflow liquid chromatography on an EASY-nLC system (Thermo Fisher Scientific, Bremen, Germany) on-line coupled to an Q Exactive HF or QExactive 240 quadrupole orbitrap mass spectrometer (Thermo Fisher Scientific). Samples were loaded onto a 50 cm column with 75 µmm inner diameter, in-house packed with 3 µm reversed-phase silica beads (ReproSil-Pur C 18 -AQ, Dr. Maisch GmbH, Germany). Separated peptides were electrosprayed into mass spectrometer with a linear gradient of 5% to 50% ACN in 0.5% acetic acid over 120 min at a constant flow of 300 nL/min, followed by a wash with up to 95% ACN. The mass spectrometer operated in a data-dependent acquisition mode alternating between one full scan and MS/MS scans of abundant peaks (i.e., Top 15 method). Full scans (m/z 300-2000) were acquired in the Orbitrap analyzer with a resolution of 60,000 at 100 m/z or 120,000 at 200 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Mass spectrometry raw data files were processed using MaxQuant software (v. 1.6.2.10) 74 . The derived peak list was incorporated with the Andromeda search engine against the reference C. neoformans var. grubii serotype A (strain H99/ATCC 208821) proteome (7430 sequences; Oct. 2018) and Mus musculus (55,462 sequences; Oct 2018) from Uniprot 75 . The parameters were as follows: trypsin enzyme specificity allowing for a maximum of two missed cleavages, seven amino acid minimum required peptide length, fixed modification of cysteine carbamidomethylation, variable modifications of methionine oxidation and N-acetylation for proteins. A target-decoy approach filtered peptide spectral matches with a false-discovery rate (FDR) of 1%, with a minimum of two peptides required for protein identification. Relative label-free quantification (LFQ) and match between runs enabled, and the MaxLFQ algorithm used a minimum ratio count of 1 76 . Split by taxonomic ID enabled when two proteome FASTA files were inputted in the same experiment (e.g., C. neoformans and M. musculus). Statistical analysis and data visualization of MaxQuant-processed data was performed using Perseus software (v. 1.6.2.2) 77 . First, data were prepared by filtering for reverse hits to the database, contaminants, and proteins only identified by site, followed by log 2 transformation of LFQ intensities. Filtering for valid values (valid-value filter of 3 in at least one group) and missing values were imputed from the normal distribution (width, 0.3 standard deviations (SD); downshift, 1.8 SDs). Significant differential abundance of proteins identified by Student’s t-test (P ≤ 0.05) with multiple-hypothesis testing correction using the Benjamini-Hochberg FDR cutoff at 0.05 with S 0 = 1."],"omics_type":["Proteomics"],"labhead":["Jennifer Geddes-McAlister"],"instrument_platform":[""],"labhead_affiliation":["Molecular and Cellular Biology, University of Guelph, Canada"],"submission_type":["PARTIAL"],"species":["Cryptococcus Neoformans Var. Grubii Serotype A (strain H99 / Atcc 208821 / Cbs 10515 / Fgsc 9487) (filobasidiella Neoformans Var. Grubii)","Mus Musculus (mouse)"],"publication":["Not available"],"submitter_mail":["jgeddesm@uoguelph.ca"],"submitter_affiliation":["University of Guelph"],"submitter_country":["Canada"],"additional_accession":[]},"is_claimable":false,"name":"Cryptococcal infectome uncovers new therapeutic targets","description":"Mortality and morbidity rates of invasive fungal infections are rising as new pathogens emerge, antifungal resistance rates rise, and susceptible populations increase in numbers. Innovative strategies to identify and characterize novel druggable targets and investigate mechanisms of action driving fungal virulence and survival are urgently needed. For Cryptococcus neoformans, a human fungal pathogen with global distribution and elevated infectivity rates, especially among immunocompromised individuals, elucidation of mechanistic drivers of infection are limited. In this study, we developed an innovative pipeline to explore fluctuations in the fungal infectome combined with phenome fingerprinting to define three categories of putative fungal therapeutic candidates: antifungal, anti-virulence, and infection-relevant. Prioritization of an uncharacterized, conserved, and virulence-associated protein, CipC, explored distinct signatures of extracellular vesicles and pointed towards enhanced antigenic properties. A murine immunization trial revealed limited heightened protection with EVs from a deletion strain of cipC; however, an increased and diversified host immune response was observed, supporting a putative role in pan-fungal immunization. We report a comprehensive pipeline to define and explore novel drivers of fungal infectivity for the identification of new therapeutic targets to improve current treatment and protections strategies against fungal pathogens.","dates":{"publication":"2026-05-20","submission":"2024-04-17"},"accession":"PXD051506","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:544496","NEWT:5180","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:4081","NEWT:876138","NEWT:554","NEWT:98334","NEWT:237561","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:3880","NEWT:8782","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:9796","NEWT:725","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:29760","NEWT:260705","NEWT:80863","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:6282","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1182590","NEWT:8726","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:4120","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:4113","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:3708","NEWT:106592","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:4909","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:145943","NEWT:3635","NEWT:235443","NEWT:1480154","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:573","NEWT:7091"],"ORCID":["0000-0002-4257-2096"]}}