There is a difference in the content of glomerular filtrate and urine.

Glomerular filtrate contains all contents of blood plasma except the protein part. After that reabsorption of the filtrate to obtain amino acids, ions like Na+, nutrients and water occur in the proximal and distal convoluted tubules. So this composition of urine (filtrate) is different from the originally obtained glomerular filtrate. Some ions are constantly added to this fluid to maintain the pH and osmotic balance.

The glomerular filtrate is formed at the first step of the urine formation in the Bowman's capsule while urine is formed at the end of the nephron.