Comparative study of mass spectrometry data analysis software for phosphoproteomics using DIA

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Mass spectrometry-based phosphoproteomics is a key method to identify protein phosphorylations that may be involved in pathologies by regulating signal transduction pathways, cell growth and cell differentiation. However, mass spectrometry datas are complex to analyze and requires powerful calculation softwares to identify post translational modifications (PTMs). Throughout this study, we tried to determine the best tools to analyse phosphoproteomes by first comparing former version of DIA-NN software with the latest version released (V.2.0.2), which has been improved to analyse protein phosphorylations. We then decided to compare DIA-NN and Spectronaut softwares which are the most commonly used for DIA analysis, on various aspects such as identification and quantification, analysis time and the probability and accuracy of phosphorylated sites localization. To complete the study, we compared the DIA results from DIA-NN and Spectronaut with DDA results from MSFragger and Maxquant on the same samples in terms of class I phosphosite content.

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