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A multicenter study benchmarks software tools for label-free proteome quantification
A guided tour of the Trans-Proteomic Pipeline
Mass spectrometry-based proteomics and network biology
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
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