Thylakoids contain many integral and peripheral membrane proteins, as well as lumenal proteins. Recent proteomics studies of thylakoid fractions have provided further details on the protein composition of the thylakoids. These data have been summarized in several plastid protein databases that are available online.
According to these studies, the thylakoid proteome consists of at least 335 different proteins. Out of these, 89 are in the lumen, 116 are integral membrane proteins, 62 are peripheral proteins on the stroma side, and 68 peripheral proteins on the lumenal side. Additional low-abundance lumenal proteins can be predicted through computational methods. Of the thylakoid proteins with known functions, 42% are involved in photosynthesis. The next largest functional groups include proteins involved in protein targeting, processing and folding with 11%, oxidative stress response (9%) and translation (8%).