Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses

Samuel Wieczorek (1) , Quentin Giai Gianetto (2, 3) , Thomas Burger (1)

1 EDyP - Etude de la dynamique des protéomes
2 Département de Biologie Computationnelle - Department of Computational Biology
3 UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology

Results from mass spectrometry based quantitative proteomics analysis correspond to a subset of proteins which are considered differentially abundant relative to a control. Their selection is delicate and often requires some statistical expertise in addition to a refined knowledge of the experimental data. To facilitate the selection process, we have considered differential analysis as a five-step process, and here we present the practical aspects of the different steps. Prostar software is used throughout this article for illustration, but the general methodology is applicable with many other tools. By applying the approach detailed here, researchers who may be less familiar with statistical considerations can be more confident in the results they present.

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]

Samuel Wieczorek, Quentin Giai Gianetto, Thomas Burger. Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses. Journal of Proteomics, 2019, 207, pp.103441. ⟨10.1016/j.jprot.2019.103441⟩. ⟨hal-02267178⟩