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bioRxiv · 10.1101/2025.11.17.687597

Pho-Tip: one-pot dephosphorylation for rapid and sensitive analysis of DIA phosphoproteomics data

Faisst, K. D.·Lau, K.·Sinn, L. R.·Szyrwiel, L.·Demichev, V.
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Abstract

Recent advances in instrumentation and data processing have transformed data-independent acquisition (DIA) proteomics into a reliable technology for quantitative profiling of post-translational modifications. However, analysis of DIA phosphoproteomics data is challenging due to the large search space, wherein all combinations of phosphosites on a peptide need to be considered. Current approaches therefore face significant hurdles in detecting low-abundant phosphorylated peptides, in particular when working with low sample amounts. Here we introduce Pho-Tip, a lossless one-pot dephosphorylation strategy. We show that Pho-Tip enables comprehensive mapping of phosphorylated peptide sequences, facilitating streamlined creation of experiment-focused in silico predicted spectral libraries and thus rapid and sensitive analysis of DIA phosphoproteomics experiments.

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Faisst, K. D., Lau, K., Sinn, L. R., Szyrwiel, L., Demichev, V.. 2025-11-18. Pho-Tip: one-pot dephosphorylation for rapid and sensitive analysis of DIA phosphoproteomics data. https://doi.org/10.1101/2025.11.17.687597

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