There are different ways you can cook linseed. If you wish to incorporate it in pastries, you can sprinkle whole seeds on the dough to enhance the texture and give it a nutty punch. On the other hand, you can use it as an egg alternative by adding some water and letting it get the required consistency before putting it into your dish. As for soup thickening, you need to mix with water and add to your pot. However, the boiled seed can be taken as a top dressing for salads and desserts. Cooking linseed does not damage the nutrients in these seeds. Therefore, you will still get your proteins, whichever method you use to enjoy it. Amino acids are also not damaged by cooking the seeds for some time.