Data files generated within the project described in the paper: “Expressed protein profile of a “Candidatus Entotheonella”-like bacterium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics”. Data is organized in two zip archives <b.1_Raw_data.zip and 2_Processed_data.zip. Contents of the archives 1_Raw_data.zip:The directory peaks_exports contains the information related to the de novo sequencing of the peptides. There is one subdirectory for each sample (10 in total). Each sample subdirectory contains 5 files:

DB search psm.csv: Output of the database search including post-translational modifications (PTM) de novo only peptides.csv: Features of de novo peptides only peptide.csv: Features of peptides identified protein-peptides.csv: Features of peptides matching proteins in the database proteins.csv: Features of all identified proteins

2_Processed_data.zip:The archive contains two subfolders: 1_Assemblies_databases: Metagenomic assemblies (contigs > 1 Kbp) used as a database for matching sequenced peptides. There are two, one for the sponge aply_sponge_1k_aa.faa, and one for the seawater sw_1k_aa.faa 2_Protein_fastas: Includes the actual input for the analyses presented, and similarly is divided into two subfolders: Seawater_Mediterranean, containing four files, one for each seawater sample analyzed; and Sponge_Aplysina_aerophoba which includes six files, one for each sponge sample analyzed.All files are named according to sample identifiers provided in the manuscript, namely:

DB search psm.csv: Output of the database search including post-translational modifications (PTM) proteins_16B.fasta (Sponge Aplysina aerophoba) proteins_16C.fasta (Sponge Aplysina aerophoba) proteins_17.fasta (Sponge Aplysina aerophoba) proteins_19A.fasta (Sponge Aplysina aerophoba) proteins_19B.fasta (Sponge Aplysina aerophoba) proteins_25.fasta (Sponge Aplysina aerophoba) proteins_sw5.fasta (Mediterranean seawater) proteins_sw6.fasta (Mediterranean seawater) proteins_sw7.fasta (Mediterranean seawater) proteins_sw8.fasta (Mediterranean seawater)