At the moment you cannot apply CIS deductions to Quotes, however we have do have a workaround which will allow you to calculate and apply CIS to a quote.
Raise an invoice which replicates the quote totals and apply the CIS deduction. Then, click the Copy button towards the bottom right of the screen and select Copy to new Quote. Now, the totals with the deductions will be added to a new quote. You can now simply delete the original invoice.