Enable temporary proxy for apt-get by editing (create it if not exist /etc/apt/apt.conf and add the line (change username, password, host and port):
Install the tsocks application:
sudo apt-get install tsocks
Remove the line added in the step before from from /etc/apt/apt.conf
Edit the /etc/socks.conf file and change the default server to the IP address of your socks server (a domain name does not work!); if applicable also change the port number for your socks connection.
Now to use this new socks proxy go ahead and execute:
sudo tsocks apt-get update
Even though you have removed the proxy settings from the /etc/apt/apt.conf file this should still update your apt list.