Table II Nano-LC-MS/MS instruments
Mass spectrometerQ Exactive (Q-E)Orbitrap EliteOrbitrap Velos Pro
HPLCThermo EASY-nLC 1000Eksigent nanoLC Ultra-2D plusThermo EASY-nLC 1000
Pre-columnAcclaim® PepMap 100 pre-column75 μm × 2 cm, 3 μm ReproSil-Pur 120 C18-AQ (Dr. Maisch GmbH, Germany)
Analytical columnAcclaim® PepMap RSLC column75 μm × 15 cm, 1.9 μm ReproSil-Pur 120 C18-AQ (Dr. Maisch GmbH, Germany)75 μm × 15 cm, 3 μm ReproSil-Pur 120 C18-AQ (Dr. Maisch GmbH, Germany)
MS resolution70,00060,00060,000
MS automatic gain control target1e61e61e6
MS/MS HCD resolution17,50015,00015,000
MS/MS automatic gain control target1e5HCD, 5e4; CID, 1e4HCD, 5e4; CID, 3e4
MS/MS normalized collision energy35.0HCD, 37.5; CID, 40.0HCD, 36.0; CID, 40.0
  • Listed are three instrument setups and settings for MS runs. For Elite and Velos, both high-energy C-trap dissociation (HCD) and collision-induced dissociation (CID) were used for MS/MS scans.