Direct empirical in-house assessment of peptide proteotypicity for targeted proteomics

Butenko, I. O.; Kitsilovskaya, N. A.; Vakaryuk, A. V.; Lazareva, A. A.; Gremyacheva, V. D.; Kovalenko, A. V.; Lebedeva, A. A.; Baraboshkin, N. M.; Chudinov, I. K.; Khchoian, A. G.; Kurylova, O. V.; Gorbunov, K. S.; Pavlenko, A.; Kozhemyakin, G. L.; Fedorov, O. V.; Ilina, E.; Govorun, V. M.

doi:10.64898/2026.02.22.699713

bioRxiv · 10.64898/2026.02.22.699713

Direct empirical in-house assessment of peptide proteotypicity for targeted proteomics

Butenko, I. O.·Kitsilovskaya, N. A.·Vakaryuk, A. V.·Lazareva, A. A.·Gremyacheva, V. D.·Kovalenko, A. V.·Lebedeva, A. A.·Baraboshkin, N. M.·Chudinov, I. K.·Khchoian, A. G.·Kurylova, O. V.·Gorbunov, K. S.·Pavlenko, A.·Kozhemyakin, G. L.·Fedorov, O. V.·Ilina, E.·Govorun, V. M.

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Abstract

In bottom-up proteomics peptide it was early shown that despite a certain protein is present in a sample, only a subset of its proteolytic peptide products will be detected with LC-MS analysis. Property of peptide being frequently detected given its source proteins identification was called proteotypicity. Much effort has been since applied to predict proteotypic peptides and summarize evidence on peptide detection. Nevertheless, when targeted proteomics method is being developed, prediction or inference from communal experience might be inaccurate and prior knowledge of true peptide proteotypicity in a selected setup for a selected population is necessary. In this work we test fully in-house approach for proteotypicity assessment including comprehensive peptide synthesis and detection verification. Proteotypicity and contribution of sample processing and biology-related factors are estimated in a model experiment for three plasma proteins, albumin, ceruloplasmin and C-reactive protein.

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Butenko, I. O., Kitsilovskaya, N. A., Vakaryuk, A. V., Lazareva, A. A., Gremyacheva, V. D., Kovalenko, A. V., Lebedeva, A. A., Baraboshkin, N. M., Chudinov, I. K., Khchoian, A. G., Kurylova, O. V., Gorbunov, K. S., Pavlenko, A., Kozhemyakin, G. L., Fedorov, O. V., Ilina, E., Govorun, V. M.. 2026-02-23. Direct empirical in-house assessment of peptide proteotypicity for targeted proteomics. https://doi.org/10.64898/2026.02.22.699713

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