Data Analysis Using MaxQuant

Raw files were processed using MaxQuant (version 1.614.0). The database search was performed against the Synechocystis sp. PCC 6803 Uniprot database (UP000001425 3507) entries using Andromeda as a search engine. Cysteine carbamidomethylation was set as a fixed modification and methionine oxidation, protein N-term acetylation, and phosphorylation of serine, threonine, and tyrosine were set as variable modifications. Trypsin was specified as enzyme and up to two miss cleavages were allowed. Filtering was done at 1% false discovery rate (FDR) at the protein and peptide level. Label-free quantification (LFQ) was performed and quantified data were processed and analyzed using R and Perseus (Tyanova et al., 2016). Processed data can be found in Supplementary Table 2.