1. Conventional-Flow Liquid Chromatography–Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses
- Author
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Magdalena Proksova, Ondřej Soukup, Vojtěch Tambor, Jana Klimentova, Kristýna Pimková, Marie Vajrychova, Marketa Benkova, and Juraj Lenčo
- Subjects
Proteomics ,0301 basic medicine ,Chromatography ,Chemistry ,010401 analytical chemistry ,Proteins ,Mass spectrometry ,01 natural sciences ,Mass Spectrometry ,0104 chemical sciences ,Analytical Chemistry ,03 medical and health sciences ,Targeted proteomics ,030104 developmental biology ,Liquid chromatography–mass spectrometry ,Humans ,Chromatography, Liquid ,HeLa Cells - Abstract
Due to its sensitivity and productivity, bottom-up proteomics based on liquid chromatography-mass spectrometry (LC-MS) has become the core approach in the field. The de facto standard LC-MS platform for proteomics operates at sub-μL/min flow rates, and nanospray is required for efficiently introducing peptides into a mass spectrometer. Although this is almost a "dogma", this view is being reconsidered in light of developments in highly efficient chromatographic columns, and especially with the introduction of exceptionally sensitive MS instruments. Although conventional-flow LC-MS platforms have recently penetrated targeted proteomics successfully, their possibilities in discovery-oriented proteomics have not yet been thoroughly explored. Our objective was to determine what are the extra costs and what optimization and adjustments to a conventional-flow LC-MS system must be undertaken to identify a comparable number of proteins as can be identified on a nanoLC-MS system. We demonstrate that the amount of a complex tryptic digest needed for comparable proteome coverage can be roughly 5-fold greater, providing the column dimensions are properly chosen, extra-column peak dispersion is minimized, column temperature and flow rate are set to levels appropriate for peptide separation, and the composition of mobile phases is fine-tuned. Indeed, we identified 2 835 proteins from 2 μg of HeLa cells tryptic digest separated during a 60 min gradient at 68 μL/min on a 1.0 mm × 250 mm column held at 55 °C and using an aqua-acetonitrile mobile phases containing 0.1% formic acid, 0.4% acetic acid, and 3% dimethyl sulfoxide. Our results document that conventional-flow LC-MS is an attractive alternative for bottom-up exploratory proteomics.
- Published
- 2018
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