In the salsa canning classes from MU Extension's food preservation series, many participants ask if they can use their own recipe to can salsa. The answer to that is no, due to safety reasons.
Salsas are a mix of low acid (peppers, onions) and mid- to high-acid (tomatoes, lemon juice/vinegar) ingredients. If the proportion of those is off and the salsa is not acidic enough, botulism can survive the canning process and possibly make someone sick. Botulism does not like an acidic environment, so it is vital to make sure we follow a tested recipe with enough acidity to safely can our salsa in a boiling water bath canner. That's why low-acid foods are canned in a pressure canner, the temperature is much higher and will kill any botulism spores. Acidic foods (like a tested salsa recipe, as well as fruits, jams/jellies, pickles) can be canned in a boiling water bath canner. The National Center for Home Food Preservation has more information about safety on their "Ensuring Safe Canned Foods" webpage.
It is only recommended to use a tested recipe to can salsa, such as one from Ball Blue Book, USDA, National Center for Home Food Preservation, or a state Cooperative Extension (like University of Missouri Extension). It is perfectly fine to make your own recipe and freeze the salsa, or eat it fresh.
There is no inexpensive way to test homemade salsa recipes, but recently the National Center for Home Food Preservation tested and released a "choice" salsa recipe.
This recipe uses 6 cups of tomatoes, 9 cups of peppers/onions (you can choose the types of onions and peppers and what combination you want, but it must equal 9 cups), 1 1/2 cups of commercial lemon juice, and 3 teaspoons canning or pickling salt. Make sure you read through all of the instructions to properly prepare the ingredients.
You must also know your altitude before using a boiling water bath canning because the processing time will vary depending on altitude. In Missouri, you can find a map of the altitudes on the MU Extension guide sheet, "Before You Start to Can, Learn the Basics."
National Center for Home Food Preservation
National Center for Home Food Preservation choice salsa recipe
MU Extension Home Food Preservation guide sheets
MU Extension Tantalizing Tomatoes guide sheet