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Is there any capital expenditure in the accounts eg new instruments?
Not correct, depreciation and tax have nothing to do with one another. You should have claimed Capital Allowances and your Annual Investment Allowance (AIA), ie the cost of the new equipment, ia allowed at 100%.
Yes depreciation is a way of charging an asset over its anticipated working life. For taxation capital allowances rule, OK!
It is highly likely that two tax offices were both giving you a personal allowance resulting in an under deduction of tax and this was the resultant recovery.
That would appear tobe the vase.
Thank you for your support.