Yes, there are differences if there's something in the path that the audio data is taking that "screws" with it before it comes out of your USB port. That can be a player software with integrated resamplers, EQ, or mixers, an operating system's own or a third party's system-wide audio mixer that you installed knowingly or unknowingly, etc.
If there isn't, though, the data that comes into the DAC is exactly the same. And in those cases, the analog output sounds and measures precisely the same, regardless of the source or the storage medium.
And just to be abundantly clear: This doesn't necessarily have to apply to a 16 bit 44.1 stream from a streaming service when compared to that same album's CD, for example. It can be the same, but depending on whether any processing happened on the label's or streaming services' end, it doesn't necessarily have to be the same. My tests and the results I saw only apply to comparisons between CDs I own and bit-perfect rips I personally made of those very CDs.