Using long columns to quantify over 9200 unique protein groups from brain tissue in a single injection on an Orbitrap Exploris 480 mass spectrometer

Abstract

The most exciting advancement in LC-MS/MS-based bottom-up proteomics has centered around enhancing mass spectrometers. Among these, the latest and most advanced mass spectrometer for bottom-up proteomics is the Orbitrap Astral that has the highest scan rate to accelerate throughput and the highest sensitivity to handle a very small amount of peptide samples and to achieve deeper proteomics. However, its affordability remains a challenge for most laboratories. While significant strides have been made in improving mass spectrometry, advancing liquid chromatography (LC) to achieve deeper proteomics has not achieved significant successes since the innovation of Multidimensional Protein Identification Technology (MudPIT) in 2001. To achieve deeper proteomics in a less labor-intensive and more reproducible approach while using a more cost-effective mass spectrometer, such as the Orbitrap Exploris 480, we evaluated trap columns as long as 40 cm and analytical column as long as 600 cm besides sample loading amount, gradient time, and analytical column particle size to enable a fractionation-free method for a single injection to obtain deeper proteomics. The length of trap and analytic columns is the key factor. Using a 30 cm trap column and 250 cm analytical column with other optimized LC conditions, we quantified over 9200 unique protein groups from brain tissue in a single injection using a 24-h gradient on an Orbitrap Exploris 480 mass spectrometer.