。
She was breathing heavily, shoulders heaving.
Literal
She [topic-は] shoulders [with-で] breath [object-を] was-doing.
肩で息をする — literally 'to breathe with one's shoulders' — is the standard idiom for the visibly labored breathing you do after running, climbing stairs, or recovering from shock. The で is instrumental, marking 'shoulders' as the means of breathing. It's a vivid expression because it captures the physical fact: when you're truly winded, your whole upper body lifts with each breath. Pair it with 肩で息をしている and you've described someone gasping; freeze-framed in the past with ~ていた, the camera holds on them mid-pant.