Mi-Youn Brusniak

TL;DR: The ProteoWizard Toolkit is developed, a robust set of open-source, software libraries and applications designed to facilitate proteomics research that implements the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats.

TL;DR: In this article, the authors present mProphet, a fully automated system that computes accurate error rates for the identification of targeted peptides in SRM data sets and maximizes specificity and sensitivity by combining relevant features in the data into a statistical model.

TL;DR: An overview of the main quantification principles and available software solutions for the analysis of data generated by liquid chromatography coupled to mass spectrometry (LC-MS) serves as a starting point for researchers to choose an appropriate software solution for quantitative proteomic experiments.

TL;DR: An open source software tool, SuperHirn, that comprises a set of modules to process LC‐MS data acquired on a high resolution mass spectrometer, which automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.

TL;DR: A system-wide analysis of protein phosphorylation in yeast reveals robustness in the network of kinases and phosphatases and reinforces the idea that simple linear representations of signaling pathways might be insufficient for drug development and for describing organismal homeostasis.