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Skyline

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A freely-available and open source Windows client application for building selected reaction monitoring (SRM)/multiple reaction monitoring (MRM), parallel reaction monitoring (PRM - targeted MS/MS), data independent acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. Skyline aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.

Ariadne

Offers reliable and automated analysis of large-scale SRM differential expression studies. To quantify monitored targets, Ariadne exploits metadata imported from the transition lists, and targets can be filtered according to mProphet output. Signal processing and statistical learning approaches are combined to compute peptide quantifications. To robustly estimate absolute abundances, the external calibration curve method is applied, ensuring linearity over the measured dynamic range.