Raw mass spectrometry Thermo data from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"

The LacI target purification experiments were performed on a nanoflow LC system, EASY-nLC II coupled to a hybrid linear ion trap Orbitrap Classic mass spectrometer equipped with a Nanospray Flex Ion Source (Thermo Fisher Scientific). All other measurements were performed on a hybrid ion trap-Orbitrap Elite mass spectrometer (Thermo Fisher Scientific), which provided greater detection sensitivity and other fragmentation techniques as described.

The Orbitrap was operated in data-dependent acquisition mode to automatically alternate between a full scan (m/z=400–1,800) in the Orbitrap (resolution 120,000) and subsequent 5 MS/MS scans also acquired in Orbitrap with 15,000 resolution. The MS/MS spectra were acquired for the top 5 ions alternating between higher collision dissociation (HCD) and electron transfer dissociation (ETD) fragmentations that are well suited for higher charge peptides.