Raw Data pertaining to the Analysis of Seawater Chemical Diversity in Mediterranean Underwater Sea Caves

This folder contains the raw data associated to the research article describing the seawater chemical composition of four selected Mediterranean sea caves. Samplings were performed in semi-dark (S) and dark (D) communities of each cave. Two series of experiment were conducted (EXP1, in situ and EXP2 in aquaria). 

Raw MS data were also deposited on Massive (https://massive.ucsd.edu/) under the following identifier MSV000097503 for EXP1, and MSV000097504 for EXP2.

 This folder contains:

the raw mass spectrometry (MS) data in open mzXML format 

the metadata explaining the identity of each samplings for EXP1 and EXP2

the excel spreadsheet of annotated chemical features that were significantly more represented in S and D sampled seawater. These features are organized per molecular entities. This excel was used to build the Figures 3, 4, 6 of the compiled research article and in supporting information. File name = MS-data annotations

the csv file used to build the volcano plot (Figure 3 in the manuscript)

the spectral data as mgf files for putatively identified sponge specialized exometabolites (Figure 7 and supporting information).

Remarks:

All MS2 data were acquired on a Bruker Impact II qTOF (ESI positive, collision energy 20-40eV) at the Metabolomics and Natural Product facility within IMBE

SIRIUS software and CANOPUS (see below) were used to further annotate the chemodiversity of captured marine molecules.

References related to in silico MS annotation tools:

·     Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nature Biotechnology, 2020.  https://doi.org/10.1038/s41587-020-0740-8

·      Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart ClassyFire: automated chemical classification with a comprehensive, computable taxonomy J Cheminf, 8, 2016.  https://doi.org/10.1186/s13321-016-0174-y

·     Kim, Hyun Woo and Wang, Mingxun and Leber, Christopher A. and Nothias, Louis-Félix and Reher, Raphael and Kang, Kyo Bin and van der Hooft, Justin J. J. and Dorrestein, Pieter C. and Gerwick, William H. and Cottrell, Garrison W. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. Journal of Natural Products, 84, 2021. https://doi.org/10.1021/acs.jnatprod.1c00399