At To-Done, Bob Walsh has written a 2 parts of article about using Google Desktop to help on your GTD system. He concentrated using Google Desktop on Emails in Outlook and show some quick ways on searching the archive of emails. On the second part, he talks about how not to get interrupted by setting Google Desktop to track new email, instead having notification to break your flow:

… Being a writer, a micro-ISV and a contract programmer, I can’t afford to be cattle prodded out every five minutes out as I’m coding or writing: a slew of these interruptions completely ruin a Flow (more on what I call Butterfly Stroke Productivity in a future post here.). So I’ve set Outlook to never interrupt me as a rule.

But on the other hand, there are times when you damn well better be ready to respond to an email, heads down being productive or not. So, how are you going to know about a must-read email from a client, or God Forbid, an Editor? Google Search in Sidebar mode is the answer …

GTD and Google Desktop, Part 1: Outlook
GTD and Google Desktop, Part 2

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