DIANA - algorithmic improvements for analysis of data-independent acquisition MS data

MOTIVATION Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification. RESULTS We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. AVAILABILITY AND IMPLEMENTATION DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.