Systematic internal standard selection for capillary liquid chromatography-mass spectrometry time normalization to facilitate serum proteomics.

Because blood interacts with almost all tissues of the body, it is likely that changes in the overall health of an organism will be reflected in the quantities of specific serum peptides and proteins, making them biomarkers. Due to the complexity of serum, pre-analytical sample simplification and separation are needed prior to mass spectrometric analysis. Use of a reverse-phase capillary column coupled to a mass spectrometer allows for separation and analysis of serum as part of efforts to discover biomarkers. Even after sample simplification by organic solvent precipitation, data files for a single sample typically exceed one gigabyte, making it difficult to analyze complete serum mass spectrometry profiles with currently available software. However, with adequate safeguards, it appears possible to consider portions of mass spectra to find differences in peak intensities between clinical comparison groups visually. To facilitate this, the elution profile was divided into 2-min intervals in which mass spectrometry data were averaged. This required that molecular species had defined reproducible elution times. Given liquid chromatography coupled to mass spectrometry variation, misalignment of elution times of individual peaks occurred often. Hence, internal time controls were identified within each window and used for elution time normalization. This significantly reduced variability in data. This approach allowed for peak alignment across samples, improving biomarker discovery.