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Where should I put a citation mark when the cited information is only the second part of a sentence? This was my first attempt,

Thus, fuel mass is more sensitive to payload mass changes for faster trajectories due to higher Δv values [1].

but as I re-read it I thought it may give the impression that the citation regards the whole sentence. In this case, the piece of information that is cited is "faster trajectories have higher Δv values".

Is there a better way of re-writing this, or is it not that misleading?

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It is a bit misleading; you don't want to imply that the cited author said something s'he didn't. The easiest solution might be to invert the clauses:

Faster trajectories have higher Δv values [1], thus fuel mass is more sensitive to payload mass changes.

If you need to keep that basic structure, then you might separate out the citation as a parenthetical:

Thus, fuel mass is more sensitive to payload mass changes for faster trajectories (faster trajectories have higher Δv values, per [1]).

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