RNA pull-down coupled with LC-MS/MS was performed to identify proteins interacting with lncRNA GIRGL in A549 lung adenocarcinoma cells. Biotin-labeled sense and antisense GIRGL probes were used to capture protein complexes, followed by SDS-PAGE separation and in-gel digestion. Peptides were analyzed by LTQ-Orbitrap mass spectrometry and searched against the UniProt human database. This dataset supports the identification of YBX1 as a GIRGL-interacting protein.