A method for processing data of an analytical instrument for analyzing biological samples, the method comprising: receiving instrument data from the analytical instrument (1a; 1b) at a data processing module (2; 2a; 2b) communicatively connected with the analytical instrument (1a; 1b); generating metadata from the received instrument data at the data processing module, wherein generating the metadata refers to extracting data from the instrument data, with or without additional processing steps; applying a first encryption to the instrument data at the data processing module (2; 2a; 2b), thereby to obtain encrypted instrument data; applying a second encryption to the generated metadata at the data processing module (2; 2a; 2b), thereby to obtain encrypted metadata, wherein applying the first encryption comprises using a first encryption key and wherein applying the second encryption comprises using a second encryption key different from the first encryption key, wherein the second encryption key is an encryption key of a party operating a remote server through which the encrypted instrument data shall be sent; transmitting the encrypted metadata and the encrypted instrument data to a remote server, wherein the remote server and the data processing module are communicatively connected; removing the second encryption from the metadata at the remote server; extracting the metadata at the remote server; processing the metadata at the remote server for monitoring of the analytical instrument or for quality control purposes of the analytical instrument (1a; 1b) forwarding the instrument data encrypted by the first encryption from the remote server to a management system of the analytical instrument; and removing the first encryption at the management system to process the instrument data. receiving instrument data from the analytical instrument (1a; 1b) at a data processing module (2; 2a; 2b) communicatively connected with the analytical instrument (1a; 1b); generating metadata from the received instrument data at the data processing module, wherein generating the metadata refers to extracting data from the instrument data, with or without additional processing steps; applying a first encryption to the instrument data at the data processing module (2; 2a; 2b), thereby to obtain encrypted instrument data; applying a second encryption to the generated metadata at the data processing module (2; 2a; 2b), thereby to obtain encrypted metadata, wherein applying the first encryption comprises using a first encryption key and wherein applying the second encryption comprises using a second encryption key different from the first encryption key, wherein the second encryption key is an encryption key of a party operating a remote server through which the encrypted instrument data shall be sent; transmitting the encrypted metadata and the encrypted instrument data to a remote server, wherein the remote server and the data processing module are communicatively connected; removing the second encryption from the metadata at the remote server; extracting the metadata at the remote server; processing the metadata at the remote server for monitoring of the analytical instrument or for quality control purposes of the analytical instrument (1a; 1b) forwarding the instrument data encrypted by the first encryption from the remote server to a management system of the analytical instrument; and removing the first encryption at the management system to process the instrument data.