An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

• Published in: Journal of the American Society for Mass Spectrometry Vol. 15; no. 2; pp. 212 - 232
• Main Authors: Belov, Mikhail E, Anderson, Gordon A, Wingerd, Mark A, Udseth, Harold R, Tang, Keqi, Prior, David C, Swanson, Kenneth R, Buschbach, Michael A, Strittmatter, Eric F, Moore, Ronald J, Smith, Richard D
• Format: Journal Article
• Language: English
• Published: New York, NY Elsevier Inc 01-02-2004; Elsevier Science; Springer Nature B.V
• Subjects: Accumulation; Amino Acid Sequence; Analytical, structural and metabolic biochemistry; Automation; Biological and medical sciences; Calibration; Capillary pressure; Chromatography; Chromatography, High Pressure Liquid; Cyclotron resonance; Cyclotrons; Deinococcus - chemistry; Deinococcus - cytology; Deviation; Downtime; Dynamic range; Electrophoresis, Capillary; Elution; Exact sciences and technology; Fourier Analysis; Fourier transforms; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; High performance liquid chromatography; High resolution; Instruments, apparatus, components and techniques common to several branches of physics and astronomy; Ions; Mass spectra; Mass spectrometers and related techniques; Mass spectrometry; Mass Spectrometry - instrumentation; Mass Spectrometry - methods; Molecular Sequence Data; Peptides; Peptides - analysis; Peptides - chemistry; Physics; Proteins; Proteomics; Proteomics - instrumentation; Proteomics - methods; Quadrupoles; Reproducibility; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Automation; Fourier transformation; Chemical analysis; Peptides; Coupled method; Instrumentation; Liquid chromatography; Ion cyclotron resonance spectrometry; Protein; Analysis method; Peptide fragment; Proteomics; Mass spectrometry
• ISSN: 1044-0305; 1879-1123
• DOI: 10.1016/j.jasms.2003.09.008

We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dual-channel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1–5% deviation in uncorrected elution times), repeatability (<20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ion-energy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10
3, and >10
5 for peptide abundances in the overall separation.