ProteoExcelTP: Development of a simple excel-based tool for surrogate peptide selection in mass spectrometry based targeted proteomics

Abstract

Selection of surrogate peptides plays a major role to achieve reproducible and accurate quantification of desired proteins in targeted proteomics. Currently, available peptide selection tools suffer from the limitation of not covering entire proteins including all the species and inflexibility in applying the exclusion criteria. Here, we have developed an excel-based ProteoExcelTP tool which can automatically select the most appropriate surrogate peptides with high flexibility in terms of addition, deletion or changing the exclusion criteria. The developed ProteoExcelTP tool has also been validated by comparison of obtained peptides from the tool with those selected in previously reported works. This is the first time to develop an excel based tool for quick and accurate selection of surrogate peptides for entire protein family of all the species. The tool is having the unique advantage of a highly user-friendly nature. It can be customized according to the specific need of the researchers. ProteoExcelTP tool will significantly enhance the throughput of the quantitative proteomic analysis. The tool can immensely help the scientists working in the field of proteomics by significantly minimizing their effort in accurate selection of surrogate peptides for quantification of endogenous proteins.