I'm working on a final year project at university which incorporates
Twitter as its primary data repository. After looking through the API
it seems that search queries are capped to 1500 posts: "Clients may
request up to 1,500 statuses via the page and rpp parameters for the
search method."

My problem originates from the fact I need to look at status tweets
over the past year on a given search query. Assuming I type in "the
pope" on Twitter Search I can only go back to 4 hours ago because of
the 1500 cap. What I have noticed however, there is a LOT of noise
(irrelevant tweets). My project is based on Natural Language
Engineering and so I need quality data.

The question I ask, how flexible is the search within the twitter API?
Could I potentially construct queries that would return the
information I need?
I only need tweets that contain the subject matter but are basically
not "spam". I need tweets about ->Real Peoples Opinions<- over the
last year.

What would be the best way to do this?

Twitter developer documentation and resources: http://dev.twitter.com/doc
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