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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:  [email protected]

Supplementary information:  Supplementary data are available at Bioinformatics online.