Application of Sequential Paired Covariance to Capillary Electrophoresis Electrospray Ionization Time-of-Flight Mass Spectrometry: Unraveling the Signal from the Noise in the Electropherogram

Abstract

The combination of capillary electrophoresis (CE) with electrospray ionization (ESI) time-of-flight mass spectrometry (TOF-MS) has recently been demonstrated. When CE is combined with TOF-MS using an electrospray interface, the method provides fast, high-resolution separations with rapid mass analysis and the potential for very high sensitivity. In analyzing the data, one first reconstructs an electropherogram from the data set and then identifies peaks in the mass spectra. The mass spectra corresponding to the peaks in the electropherogram are then inspected to enable solute identification. However, background noise often prevents detection of peaks in the reconstructed electropherogram, thus interfering with the analysis. In this work we demonstrate alternative electropherogram reconstruction techniques that enhance its signal-to-noise ratio, allowing more immediate identification of the number of components in a mixture and their corresponding retention times. The techniques described here should also be adaptable for on-line analysis of CE-ESI-TOF data and the combination with other separation techniques coupled to mass spectrometry (e.g., LC/MS), as well as any multichannel detection scheme.The combination of capillary electrophoresis (CE) with electrospray ionization mass spectrometry (ESI-MS) has proven to be a very powerful technique for solving a wide diversity of chemical, biochemical, and biomedical problems.1"5 The main advantages of capillary electrophoresis6 (i.e., speed, resolution, and the ability to handle small sample volumes) can be realized only if the mass spectrometric technique employed retains these properties while providing adequate mass resolution, detection

Capillary electrophoresis/electrospray ionization high mass accuracy time-of-flight mass spectrometry for protein identification using peptide mapping

“…8,9,22,23 One of the most commonly used techniques for protein identification by mass spectrometry is peptide mapping in conjunction with a protein database search. In order to identify a protein using a protein database, several pieces of information are needed, including the average molecular weight (MW) of the protein and the masses of several peptide fragments obtained through the enzymatic digestion of the protein of interest.…”

Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins

“…The use of laser induced fluorescence detection, which can achieve unrivalled detection limits, would enable injection of smaller sample plugs and is likely to result in the resolution of a greater number of peaks. MS identification with reconstruction of the electropherogram would also enable a greater number of peaks to be resolved (27,28). To demonstrate the potential for CE-ESI-MS of eukaryotic ribosomal proteins, the separation has also been performed with a volatile BGE, 50 mM ammonium acetate, pH 4.0 (see supplementary information †…”

Processing and classification of protein mass spectra

“…PCA separates the smoothed signals (first PCs) from noise (higher order PCs) if applied to the data matrix (Lee, Headley, & Hardy, 1991). Muddiman et al (1995) developed the sequential paired covariance (SPC) method based on the correlation between subsequent spectra as a filtering criterion, which allows suppressing noisy spectra. However, since the original signal intensities are replaced by the correlation score, quantitative information is lost in the transformed data.…”