Faims device

Dried fractions were resuspended in 0.1% FA and separated on a 500 mm, 0.075 mm Acclaim PepMap 100 C18 HPLC column (ThermoFisher, #164942) and analyzed on a Orbitrap Lumos Tribrid mass spectrometer (ThermoFisher) equipped with a FAIMS device (ThermoFisher) that was operated in two compensation voltages, −50 V and −70 V. Synchronous precursor selection based MS3 was used for TMT reporter ion signal measurements. Peptides were separated by EASY-nLC1200 using a 90 min linear gradient from 6% to 31% buffer; buffer A was 0.1% FA, buffer B was 0.1% FA, 80% ACN. The analytical column was operated at 50 °C. Raw files corresponding to the mouse livers were split on the basis of the FAIMS compensation voltage using FreeStyle (ThermoFisher). Fly fat body proteomics data were analyzed using Proteome Discoverer (version 2.4.1.15); mouse liver proteomics data were analyzed using MaxQuant (version 1.6.17.0). Isotope purity correction factors, provided by the manufacturer, were included in the analysis.

Dried fractions were resuspended in 0.1% formic acid and separated on a 50 cm, 75 μm Acclaim PepMap column (164942; Thermo Fisher Scientific) and analyzed on an Orbitrap Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) equipped with a FAIMS device (Thermo Fisher Scientific). The FAIMS device was operated in two compensation voltages, −50 and −70 V. Synchronous precursor selection based on MS3 was used for the acquisition of the TMT reporter ion signals. Peptide separation was performed on an EASY-nLC1200 using a 90 min linear gradient from 6–31% buffer; buffer A was 0.1% formic acid, and buffer B was 0.1% formic acid with 80% acetonitrile. The analytical column was operated at 50°C. Raw files were split based on the FAIMS compensation voltage using FreeStyle (Thermo Fisher Scientific).

Dried fractions were re-suspended in 0.1% FA and separated on a 50 cm, 0.075 mm Acclaim PepMap 100 C18 HPLC column (ThermoFisher, #164942) and analysed on a Orbitrap Lumos Tribrid mass spectrometer (ThermoFisher) equipped with a FAIMS device (ThermoFisher) that was operated in two compensation voltages, − 50 V and − 70 V. Synchronous precursor selection based MS3 was used for TMT reporter ion signal measurements. Peptides were separated by EASYnLC1200 using a 90 min linear gradient from 6 to 31% buffer; buffer A was 0.1%
FA, buffer B was 0.1% FA, 80% ACN. The analytical column was operated at 50 °C. Fly brain proteomics data were analysed using Proteome Discoverer (version 2.4.1.15). Isotope purity correction factors, provided by the manufacturer, were included in the analysis.