Summary: We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one. Availability: Freely available for academic use at http://pcarvalho.com/patternlab. Contact:paulo@pcarvalho.com

Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (∼250%) and unique peptides (∼30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively. Availability: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA Contact: paulo@pcarvalho.com Supplementary information: Supplementary data are available at Bioinformatics online.

Summary: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). We describe how YADA enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data. Availability: http://fields.scripps.edu/yada Contact: paulo@pcarvalho.com Supplementary information: Supplementary data are available at Bioinformatics online.