The vocabulary of theoretical statistics can be difficult to embrace from the viewpoint of
computational proteomics research, even though the notions it conveys are essential to …

Cellular functions are mediated by protein–protein interactions, and mapping the
interactome provides fundamental insights into biological systems. Affinity purification …

Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but
reproducible quantification remains challenging, especially for post-translational …

Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or
molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear …

Protein post-translational modification (PTM) regulates nearly every aspect of cellular
processes in eukaryotes. However, the identification of new protein PTMs is very …

In discovery proteomics, as well as many other “omic” approaches, the possibility to test for
the differential abundance of hundreds (or of thousands) of features simultaneously is …

Phosphoinositide 3-kinases (PI3Ks) play a central role in adaptive immunity by transducing
signals from the T cell antigen receptor (TCR) via production of PIP3. PI3Kδ is a heterodimer …

Selecting omic biomarkers using both their effect size and their differential status
significance (ie, selecting the “volcano-plot outer spray”) has long been equally biologically …

ProStaR is a software tool dedicated to differential analysis in label-free quantitative
proteomics. Practically, once biological samples have been analyzed by bottom-up mass …

Results from mass spectrometry based quantitative proteomics analysis correspond to a
subset of proteins which are considered differentially abundant relative to a control. Their …