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In an ideal world yes. But you're often lumbered with software that is already decades old and "in house" usually means developed by a self taught post grad (or undergrad if you're really unlucky). And let's not get into the fact that you have to use whatever the I instrument manufacturer provides.

Easier said than done when there's only one company that makes what you need. The government needs to break up Thermo.

A.K.A. "I've never bought specialized test/measurement equipment."

The problem is if you require well documented, available software interfaces, your available options do not exist.