XDIA (extended data-independent acquisition) is a novel approach for data acquisition in shotgun proteomics.  XDIA combines high-resolution Orbitrap survey scans with multiplexed fragmentation data using data-independent acquisition with electron transfer dissociation, collision induced dissociation, or both.  The data are then post-processed by our new software, named XDIA Processor, which enables for protein identification.

XDIA significantly increased identified spectra (~250%) and unique peptides (~30%) when compared to 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.

A search engine (e.g., ProLuCID) requires XDIA data to be previously processed by the XDIA processor to enable protein identification.

The XDIA processor requires a 2GB RAM. The GUI version is available for Windows XP SP2 and later and requires .NET 3.5 or later and is available here;.it will install in the PatternLab for proteomics directory. A command line version for Linux or Mac is available upon request for special cases.

Example data colected by XDIA and ETCaD are available here. The data can be extracted using RawExtract (RE). RE's centroid mode should be disabled for the high resolution spectra.

Any issues, please email paulo at pcarvalho.com.