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The first thing you need to be able to proofread successfully is a quiet environment where you can concentrate on what you are reading. It is best to avoid interruptions so you can be sure that you don't miss anything. Look out for homonyms, which are often missed by computer spell check programs. Homonyms are words that sound the same but have different spellings, such as 'there' and 'their'. Look out for words that might be easily confused with other words, such as 'no' and 'not'. These will also be missed by spell check programs.
If you want to have the best chance of spotting all the errors on your self published book, read the manuscript several times, looking for different errors (spelling, grammar, formatting) on each reading. Another good technique is to read sentences backwards to force you to focus on every word. Reading out loud can also be a helpful focusing technique - and it will give you a chance to hear how your words sound.