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

This contains all Thermo .raw files. 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. Higher collision dissociation was performed at a normalized collision energy of 30% and electron transfer dissociation reaction time was set to 100 msec.