Mass spectrometry (MS) has changed our understanding of health, disease, and the environment through untargeted analyses where entire molecular classes are investigated. These techniques generate huge amounts of data which when processed by statistical tools can identify important molecular features or biomarkers. The complexities of these samples are not compatible with direct introduction to the MS system and require a high-resolution separation step, typically low flow liquid chromatography (LC), prior to MS. LC columns that can produce adequate linear velocities at these low flow rates are small in volume making their results susceptible to resolution loss in extra-column volumes. Here, we investigate the implications of the extra-column effects in five LC-MS systems with triple quadrupole and orbitrap mass analyzers. The extra-column volume of these systems in their standard configuration ranged from 26.4 to 78.1 μL which we reduced to 9.57 to 18.7 μL by optimizing the fluidics. The effects of this volume reduction were assessed by studying a hydrolyzed protein sample in a proteomics environment where the intensity of the largest MS peak was improved by 1.8-3.8×. Additionally, the number of molecular features detected in the protein sample improved by up to 7.5×. The relationship between extra-column volumetric variance and flow rate shows that broadening will become much larger for MS detectors at higher flow rates, unlike a traditional small volume UV detector. The methods, applications, and theoretical insights in this work can be used to improve the mass spectrometric results of any LC-MS system.

Biomedical Research Centre University Hospital Hradec Králové Sokolská 581 Hradec Králové 50005 Czech Republic

Department of Analytical Chemistry Faculty of Pharmacy in Hradec Králové Charles University Hradec Králové 50003 Czech Republic

Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas 76019 United States

Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Králové Charles University Hradec Králové 50003 Czech Republic

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