Quantitative Accuracy in Mass Spectrometry Based Proteomics of Complex Samples: the Impact of Labeling and Precursor Interference

Biological Significance: Quantitative proteome analysis by mass spectrometry offers opportunities for biological research. However, knowing the limit of quantification in biological samples is important to accurately judge the results. By using a high-complexity sample spiked with protein standards of known concentrations, we investigated the quantification limits of label-free and label-based peptide quantification, including an evaluation of precursor mixing and its impact on quantification accuracy by isobaric labels. We suggest limits of allowed precursor interference and believe that this study contributes with information useful in proteome quantification by mass spectrometry.