Each measurement mode was pre-processed using the MetaboAnalyst web server (Version 6.0, www.metaboanalyst.ca). Data were uploaded as comma-separated value (.csv) files, with missing values being replaced with 1/5 of the minimum positive value for each feature. Raw data was log transformed to stabilize variance and reduce skewness for each RP mode separately. Features detected by multiple methods were retained from the method with the lowest number of missing values and the highest overall signal intensity.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Nuclear Magnetic Resonance (NMR) -"],"publication":["Exploration of the pathogens Candida albicans and Aspergillus fumigatus secretome using multimodal metabolomics with an emphasis on virulence factors."],"nmr_spectroscopy_protocol":["The instruments were controlled using the Bruker HyStar software and TimsControl acquisition software. Reversed-phase (RP) chromatography was used for the analysis employing an Intensity Solo 2 C18 column (100 mm × 2.1 mm, 2 µm; Bruker Daltonics) was used. The eluent system for mobile phase A was water with 0.1% formic acid, and for mobile phase B, ACN with 0.1% formic acid. The flow rate was set to 0.6 mL/min with a gradient starting at 5% B for the first 2 min, increasing to 60% B at 10 min, 98% B at 11 to 13 min, and returning to 5% B at 13.1 minutes until 15.5 min. The injection volume was 2 µL of the desalted samples.
The MS analysis for non-targeted metabolomics was performed using Parallel Accumulation Serial Fragmentation (PASEF) mode with data-dependent MS/MS acquisition and Trapped Ion Mobility Spectrometry (TIMS) stepping, following the 4D metabolomics standard method in TimsControl software (Bruker Daltonics, Bremen, Germany). The source parameters were set as follows: End Plate Offset at 500 V, Capillary Voltage at 4500 V, Nebulizer Pressure at 2 bar, Dry Gas Temperature at 230°C, Dry Gas Flow at 8.0 L/min, Sheath Gas Temperature at 400°C, and Sheath Gas Flow at 4 L/min. The specific timsTOF Pro 2 parameters included the following: Acquisition Mode in PASEF with TIMS on, Number of PASEF Ramps set to 2, Mass Range from 50–1300 Da, Mobility Range from 0.10–1.50 V·s/cm², TIMS Ramp Time at 100 ms, Collision RF at 450 Vpp, TOF Transfer Time at 65 µs, Pre-Pulse Storage Time at 3 µs, and TIMS Stepping enabled with two steps. The collision energy for fragmentation was set to 20/50 eV. RP chromatography was conducted in both negative and positive ionization mode. Mass and mobility were recalibrated using a 1:3 (v/v) mixture of sodium formate and Agilent’s ESI-L LC/MS Tuning Solution, injected at the start of each run. Additionally, a pooled QC sample (containing same amount from each sample) was used for signal correction during MS analysis.
"],"submitter_affiliation":["Tübingen university"],"submitter_name":["Sophie Tonneau"],"organism_part":["enriched culture","Culture"],"technology_type":["NMR spectroscopy assay"],"disease":[""],"extraction_protocol":["The extracts were transferred into 2 mL AFA™ Covaris glass tubes. Each sample was thoroughly mixed by vortexing with 900 μL methanol, 100 μL chloroform, and 100 μL ultrapure water before being loaded in the Covaris ultrasonicator E220 Evolution. Following extraction, solutions were loaded into a centrifuge (12,000 x g force, 30 min at 6 °C) for complete phase separation. 200 μL of each supernatant was transferred to a Covaris tube (Covaris, Woburn, USA) and placed in SpeedVac (Thermo Fisher, SPD300DDAA-230, USA) to evaporate unwanted solvents overnight. Dried pellets of polar phase solutions were resuspended in 50 μL of deuterated phosphate buffer (200 mM K2HPO4, 200 μM NaN3, pH 7.4) with 1 mM internal standard TSP
"],"organism":["Candida albicans","Aspergillus fumigatus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15942"],"author":["Nicolas Beziere. University of Tuebingen, Werner Siemens Imaging Center, Germany. nicolas.beziere@med.uni-tuebingen.de.","Denis Ispan.","Sophie Tonneau. University of Tuebingen, Werner Siemens Imaging Center, Germany. Roentgenweg 13, 72076 Tuebingen. sophie.tonneau@med.uni-tuebingen.de.","Frederic Dalle.","Gyuntae Bae.","Jannik Sprengel.","Christoph Trautwein. University of Tübingen. Christoph.Trautwein@med.uni-tuebingen.de."],"data_transformation_protocol":["MS data processing and metabolite annotation were performed using MetaboScape 2025 software (Bruker Daltonics, Bremen, Germany). Features have been extracted utilizing the program’s T-ReX-4DTM algorithm with an intensity threshold of 3000 ion counts and minimum 4D peak size of 150 points. Recursive feature extraction was activated with a minimum 4D peak size of 125 points. Metabolites were assigned by matching extracted features against target lists (Bruker HMDB Metabolite Library 2.0, METLIN-CCS Lipid Database, PNNL CCS Metabolites Database, Unified CCS Compendium 2020-03-30, Microbial Metabolites Database Version 1.0) and spectral libraries (Bruker MetaboBASE Personal Library 3.0). The annotations followed MS/MS-based level 2 confidence criteria for metabolite identification, as defined by the Metabolomics Standards Initiative 81. A match was considered if, in addition to the mass-to-charge ratio (m/z) deviation being < 2.0 ppm, at least one of the following criteria was met: mSigma < 20, MS/MS score < 900, or collision cross-section (CCS) deviation < 1%. The extracted ion chromatograms shapes were also considered. Features with intensities in study samples less than three times those observed in blanks were excluded.
The enriched cultures and monocultures were rinse two times with 5 mL pre-cooled (4 °C) PBS. PBS was removed quickly, and samples collected into 15 ml falcon tubes and pour quickly in liquid nitrogen. Samples were then directly transferred to ice. 0.8 mL of pre-chilled at -80 °C methanol was added to the falcon tubes. The samples were vortex strongly for 10 sec and placed on dry ice. All sample were stored at -80 °C until measurements.
"],"omics_type":["Metabolomics"],"study_design":["Candida albicans","Metabolomics","timsTOF LC-MS","untargeted analysis","fungal secretome","enriched culture","Bruker Avance III HD","Aspergillus fumigatus","Culture"],"curator_keywords":["Candida albicans","Metabolomics","timsTOF LC-MS","untargeted analysis","fungal secretome","enriched culture","Bruker Avance III HD","Aspergillus fumigatus","Culture"],"nmr_sample_protocol":["For comprehensive LC-MS analysis, a chromatography system (Elute Plus, Bruker Daltonics, Bremen, Germany) was coupled to a trapped ion mobility spectrometry time of flight (timsTOF) mass spectrometer (timsTOF Pro 2, Bruker Daltonics, Bremen, Germany) equipped with a vacuum insulated probe heated electrospray ionization (VIP-HESI) source. Desalting LC-MS samples were added in the amino column (500 μl), centrifuged at 12 000 x g during 5 min, then 200 μl of TSP 1mM (200 μL remaining) were added. These two steps were repeated two times. The final volume in the glass vial was 400 μl.
"],"metabolite_name":["Taurine","GTP","Lactate","Guanosine","4-Aminobutyrate","Citrate","O-Phosphoethanolamine","Creatine","ADP","O-Acetylcholine","Butyrate","Histidine","Betaine","Tyrosine","AMP","Methionine","Glycerol","Acetate","Glutamate","IMP","Carnitine","Histamine","Nicotinurate","Uridine","Hypoxanthine","Cysteine","O-Phosphocholine","2-Hydroxyglutarate","Serine","Leucine","Glycine","3-Hydroxybutyrate","myo-Inositol","Cystathionine","sn-Glycero-3-phosphocholine","scyllo-Inositol","Glutathione","Creatinine","Ethanolamine","GSSG","Creatine phosphate","Adenosine","Alanine","Phenylalanine","Aspartate","Pyroglutamate","Fumarate","Valine","Choline","Sarcosine","Asparagine","Formate","Inosine","Homocysteine","Hypotaurine","ATP","N-Acetylaspartate","NAD+","2-Hydroxybutyrate","Glutamine"],"additional_accession":[]},"is_claimable":false,"name":"Exploration of the pathogens Candida albicans and Aspergillus fumigatus secretome using multimodal metabolomics with an emphasis on virulence factors (NMR)","description":"Fungal secretome provides insight into pathogen adaptation and interspecies interactions, yet its role in mediating interaction between Aspergillus fumigatus and Candida albicans—both WHO critical-priority pathogens—remains unexplored. Using a combinatory metabolomics approach, this study profiled the secretomes of both species, identifying 176 compounds, including ten A. fumigatus mycotoxins. Exposure to C. albicans secretome altered production of several mycotoxins, notably spirotryprostatin A and sphingofungins B and D, and solid coculture assays revealed a distinct inhibition zone consistent with an antagonistic interaction between the two pathogens. Secretome exposure also shifted purine and pyrimidine biosynthesis pathways in both fungi. Some indole-derived metabolites produced by C. albicans were associated with pneumonia exacerbation. Despite these interactions, both species were able to grow together in the same space. Together, these findings suggest that these fungi can influence each other through the molecules they release and may modulate the disease progression.","dates":{"publication":"2026-10-07","submission":"2026-10-07"},"accession":"MTBLS15942","cross_references":{"MetaboLights":["MTBLC1148","MTBLC17084","MTBLC20067","MTBLC16865","MTBLC16761","MTBLC16027","MTBLC15422","MTBLC15366","MTBLC16335","MTBLC16449","MTBLC22653","MTBLC22660","MTBLC17750","MTBLC30772","MTBLC17126","MTBLC15354","MTBLC30769","MTBLC16919","MTBLC17287","MTBLC16737","MTBLC17755","MTBLC15356","MTBLC16000","MTBLC30751","MTBLC18012","MTBLC17858","MTBLC15996","MTBLC18237","MTBLC28300","MTBLC16856","MTBLC17754","MTBLC15428","MTBLC16750","MTBLC18295","MTBLC27570","MTBLC17230","MTBLC16668","MTBLC17368","MTBLC17202","MTBLC17596","MTBLC78320","MTBLC25017","MTBLC16811","MTBLC21547","MTBLC15846","MTBLC7563","MTBLC15355","MTBLC18132","MTBLC17553","MTBLC28044","MTBLC16010","MTBLC15611","MTBLC17822","MTBLC15891","MTBLC18186","MTBLC16704","MTBLC27266","MTBLC17268","MTBLC10642","MTBLC16870"],"ChEBI":["CHEBI:1148","CHEBI:17084","CHEBI:20067","CHEBI:16865","CHEBI:16761","CHEBI:16027","CHEBI:15422","CHEBI:15366","CHEBI:16335","CHEBI:16449","CHEBI:22653","CHEBI:22660","CHEBI:17750","CHEBI:30772","CHEBI:17126","CHEBI:15354","CHEBI:30769","CHEBI:16919","CHEBI:17287","CHEBI:16737","CHEBI:17755","CHEBI:15356","CHEBI:16000","CHEBI:30751","CHEBI:18012","CHEBI:17858","CHEBI:15996","CHEBI:18237","CHEBI:28300","CHEBI:16856","CHEBI:17754","CHEBI:15428","CHEBI:16750","CHEBI:18295","CHEBI:27570","CHEBI:17230","CHEBI:16668","CHEBI:17368","CHEBI:17202","CHEBI:17596","CHEBI:78320","CHEBI:25017","CHEBI:16811","CHEBI:21547","CHEBI:15846","CHEBI:7563","CHEBI:15355","CHEBI:18132","CHEBI:17553","CHEBI:28044","CHEBI:16010","CHEBI:15611","CHEBI:17822","CHEBI:15891","CHEBI:18186","CHEBI:16704","CHEBI:27266","CHEBI:17268","CHEBI:10642","CHEBI:16870"]}}