Jen,
Yes, it is possible to create a time chart using measures from a Query. However, since the time chart is study specific, it will only show measures from queries that contain the required fields: ParticipantId and ParticipantVisit. There is some help text briefly describing this requirement in the "Add Measure..." dialog from the Time Chart.

So, if for example I was writing a query in the LabKey demo study using the "Physical Exam" dataset, I would make sure to include the following two fields in my SQL:

SELECT "Physical Exam".ParticipantId,
"Physical Exam".ParticipantVisit,
...
FROM "Physical Exam"

Let me know if that doesn't work for you.
Thanks,
Cory