What is the purpose of your experiment? Analysis (e.g., IEF or PAGE) requires that most (ideally: all) proteins are extracted. Urea or thiourea can help with that. Preparative extraction requires that one particular protein is extracted as completely as possible, and in a functional state. Is your protein cytosolic or located in an organelle? Detergent can help with extraction, but also interfere with later procedures.

At any rate, you should include a buffer (about 50 mM) to keep the pH at the desired value despite the acidic content of the lysosome. You also want to keep the osmotic pressure and ion composition close to what the protein experienced in its native environment.

Thank you for your answers! I want to extract glucose transporters from muscle tissue and perform an SDS PAGE.

Since maintaining the activity of your protein is no issue, and since you are dealing with a transmembrane protein, you need detergent. SDS-sample buffer of course already has that. I'd simply try to solubilise the homogenised tissue in sample buffer, followed by a quick spin in a table-top centrifuge. If this proves unsatisfactory, I'd add some urea (5-7 M should do).

Note that for IEF (and hence 2D electrophoresis) you can solubilise only in non-ionic (Triton) and/or zwitterionic detergents (CHAPS).

Thiourea (2 M) is more expensive, but also more efficient than urea. Both may be used in combination.

Homogenisation is best done with a small Potter-Elvehjem-tube (http://www.jbc.org/content/114/2/495.short).

Thank you for your answer! Very helpful...

I used water and not a buffer, do you think my proteins will be still good or will they be damaged?

Depends on the protein. Another issue: do you want to do the first experiments w/o buffer, and the following with? Perhaps it's better to start fresh, if the samples are not too valuable.

I found muscle tissue to be very difficult to homogenise. What method are you using?

Large amounts I mince in a Warring Blendor with cooled sample vessel, small amounts with scissors. Homogenisation is then in a Potter-Elvehjem vessel of suitable size. Add the detergent only after homogenisation!