What a protein deposit is
A protein deposit is old milk soil stuck to the inside of your milk line. It shows up as shiny rainbow patches or a brown, varnish-looking stain.
Thermoduric bacteria survive hot washes and even pasteurisation, and protein is what they feed on. Deposits build up where the wash doesn't properly reach, such as the upper surfaces of the receiving can at the top of the milk line. They also build up when the wash goes cool. If the temperature drops below 55C mid-wash, fat can re-stick to the surface, and that is what leads to protein deposits and grades.
How to confirm it
Shine a torch through the milk line and look closely at the joins, low points and any dips where product can pool. Rainbow or brown film means you have a deposit. If the surface still reflects after a wash, it needs more work.
Check that the line drains fully after each wash. If it doesn't, look for a blockage or a sagging section.
What to do now
A rinse won't shift baked-on soil. The line needs flushing, scrubbing and sanitising from end to end.
Scrub the whole milk line with a milk line brush and a vat cleaner, with extra attention where you found the deposit. Don't skip the scrub if you've had a recent grade or you can see build-up.
Run a proper hot wash and sanitise through the line afterwards, and rinse out all the chemical before the next milking.
Check your jetter flow rates, flushing pulsator and air leaks. If any of them aren't performing, repair them after cleaning and before your next milking.
How to stop it coming back
Keep the wash hot. Start at 85C and stay above 55C all the way through. If it drops below 55C, stop and reheat.
Give the wash contact time. Most farm systems give 60 to 90 seconds, and the best results come from at least 8 minutes of recirculation.
Keep the water moving. Jetters need to flow properly, and air leaks reduce flow. Flushing pulsators only help when they are set up right.
Fully clean the milk line after a milk grade, and whenever water temperature has been low during previous washes.
Get the full steps
The Dairy Handbook chapter How do you fully clean a milk line? has the full clean, including when a rinse won't cut it and you need to scrub. For the difference between protein and fat soil, and how each one looks and feels, read Why do bacteria grow in your milking plant?