Label‐free quantification

For peptide identification and determination of protein intensities, MS raw data were processed using maxquant v.1.5.1.2 (Cox & Mann, 2008). The Uniprot reference proteome of N. gaditana (downloaded 12 December 2014) concatenated with randomized sequences of all entries was used for database search, with default settings for high‐resolution MS1 (Orbitrap) and low‐resolution MS2 (ion trap). Oxidation of methionine and acetylation of the protein N‐terminus were allowed as variable modifications. False discovery rate (FDR) was set to 1% at the peptide and protein level. The feature ‘match between runs’ was activated. Due to the fundamentally different protein composition of each fraction, intensity normalization by MaxQuant was omitted. Instead, normalization factors were calculated based on the sums of all non‐normalized protein intensities of each fraction.