Two months after the deadline for compliance hit, it’s now clear The Financial Times and Apple can’t come to a compromise over the new requirement that in-app subscription payments must go through iTunes Store.

The paper’s iPad and iPhone apps have disappeared from iTunes Store.

It is a blow to the FT, whose apps had processed subscription transactions independently. Last year, 10 percent of its new digital subscriptions were taken out on iPads. But the publisher says its model is premised on owning data about customers that goes through along with transactions. This was more important to it than Apple’s 30 percent take, CEO John Ridding told me recently.

It’s a more drastic move than many, including rival WSJ, had employed to work around Apple - that is, allowing iPad read access to existing subscribers but ending new in-app transactions.

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