Parallel factor analysis enables quantification and identification of highly-convolved data independent-acquired protein spectra

High-throughput data-independent acquisition (DIA) is the method of choice for quantitative proteomics, combining the best practices of targeted and shotgun proteomics approaches. The resultant DIA spectra are, however, highly convolved and with no direct precursor-fragment correspondence, complicating the analysis of biological samples. Here we present PARADIAS (PARAllel factor analysis of Data Independent Acquired Spectra), a GPU-powered unsupervised multiway factor analysis framework that deconvolves multispectral scans to individual analyte spectra, chromatographic profiles, and sample abundances, using the PARAFAC tensor decomposition method based on variation of informative spectral features. The deconvolved spectra can be annotated with traditional database search engines or used as a high-quality input for de novo sequencing methods. We demonstrate that spectral libraries generated with PARADIAS substantially reduce the false discovery rate underlying the validation of spectral quantification. PARADIAS covers up to 33 times more total ion current than library-based approaches, which typically use less than 5 % of total recorded ions, thus allowing the quantification and identification of signals from unexplored DIA spectra.