Comparison of Label Free and 18 O Labeling Mass Spectrometry in Relative Protein Quantification

Mass–spectrometry-based quantification methods have been increasingly applied to measure proteomic changes in biological systems between different physiological states. In this report, we compared two popular mass-spectrometry-based quantification strategies, stable isotope labeling and label free approaches. We spiked known amounts of standard peptides into a complex biological sample and analyzed this mixture with both stable isotope 18O labeling and label free mass spectrometry methods. We optimized data pre-processing and normalization algorithms for each method, and compared their sensitivities and accuracies. We found that both methods gave relatively accurate results, and the label free methods provided higher proteome coverage.