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Many tools in proteomics are based on accurate identification of peptide contained in a sample. In fact, the issue of identification is the foundation of the entire proteomics workflow, where all subsequent steps depend on the quality of data generated at the beginning. The accuracy of data generated allow, not only to have good results, but also to ensure consistency at the end of the analysis. There is a consensus about the factors that affect this accuracy. It is popularly assumed that exploiting physics and chemistry of peptides deduced from sequences can improve the identification accuracy. In fact, considering natural isotopes when quantifying peptides will considerably improve results. This paper presents findings that defend such a view. We explored the mass difference between the nominal mass (which considers the most abundant isotope of each element) and the mean mass (which considers the abundance of each element). We noticed that within a biomolecule, the larger the number of elements, the less this difference is negligible. In accordance with that, peptide misidentification is due to the previously explained variance. These findings reveal that including natural isotopes during quantification will play a key role in improving identification accuracy. This study could lead us to design alternative identification tools combining better sensitivity and specificity.

The Importance of Considering Natural Isotopes in Improving Protein Identiﬁcation Accuracy