Platynereis spp. were collected via snorkelling or scuba from either inside (40°43′53″N, 13°57′47″E) (stations A1-A3) or outside (40°43'33.33"N, 13°57'36.38"E and 40°44′48″N, 13°56′39″E) (stations C1-C3) the carbon dioxide (CO2) vent on the island of Ischia (Italy) and used in a reciprocal transplant experiment. The effect of exposure to high or low partial pressures of CO2 (pCO2) conditions on the proteome of worms from different pCO2 regimes was investigated to understand the effect of exposure to different pCO2 conditions on the cellular physiological response. This experiment was conducted between 04/09/2013 and 16/09/2013. The experiment was staggered during this time so all worms could be processed. After five days exposure to either low or high CO2 conditions worms were snap frozen in liquid nitrogen and shipped to the University of Hong Kong for proteomic analysis which was finalised on 02/08/2015. Proteomic profiles of worms were characterised using a liquid chromatography-mass spectrometry/mass spectrometry triple time of flight (LC-MS/ MS Triple TOF) approach.

Complete list of proteins identified in annelids Platynereis spp. from control and treatment conditions. Proteomic data were analysed in the free software Perseus (Tyanova et al., 2016) and MetaboAnalyst 4.0 (Chong et al., 2019). The proteomics analysis of Platynereis spp. led to the identification of 663 proteins, 51 of which remained for statistical analysis after the filtering step (removal of proteins with <60 % valid values). Table provides information about the mean LFQ (Label Free Quantification) intensities calculated for each protein as the best estimate satisfying all the pair-wise peptide comparisons for all analyzed experimental groups, Q-value-Andromeda output, Score-Andromeda score for the best associated MS/MS spectrum, Intensity: intenstity of the ions, MS/MS Count is spectral counting of the ions, here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide, name of proteins, number of identified peptides, UniProt accession number. (---: not applicable)