MaxDIA: Taking proteomics to the next level

A new software improves data-independent acquisition proteomics by providing a computational workflow that permits highly sensitive and accurate data analysis. Proteins are essential for our cells to function, yet many questions about their synthesis, abundance, functions, and defects still remain unanswered. High-throughput techniques can help improve our understanding of these molecules. For analysis by liquid chromatography followed by mass spectrometry (MS), proteins are broken down into smaller peptides, in a process referred to as “shotgun proteomics.” The mass-to-charge ratio of these peptides is subsequently determined with a mass spectrometer, resulting in MS spectra. From these spectra, information about the identity of the analyzed proteins can be reconstructed. However, the enormous amount and complexity of data make data analysis and interpretation challenging.

Protein ratio distributions in the four species. Credit: Max-Planck-Gesellschaft

Two main methods are used in shotgun proteomics: Data-dependent acquisition (DDA) and data-independent acquisition (DIA). In DDA, the most abundant peptides of a sample are preselected for fragmentation and measurement. This allows to reconstruct the sequences of these few preselected peptides, making analysis simpler and faster. However, this method induces a bias towards highly abundant peptides. DIA, in contrast, is more robust and sensitive. All peptides from a certain mass range are fragmented and measured at once, without preselection by abundance.

Jürgen Cox and his team have now developed a software that provides a complete computational workflow for DIA data. It allows, for the first time, to apply algorithms to DDA and DIA data in the same way. Consequently, studies based on either DDA or DIA will now become more easily comparable. MaxDIA analyzes proteomics data with and without spectral libraries. Using machine learning, the software predicts peptide fragmentation and spectral intensities. Hence, it creates precise MS spectral libraries in silico. In this way, MaxDIA includes a library-free discovery mode with reliable control of false positive protein identifications.

Source (Max-Planck-Gesellschaft. “MaxDIA: Taking proteomics to the next level.” ScienceDaily. ScienceDaily, 12 July 2021.)

Paper: Sinitcyn, P., Hamzeiy, H., Salinas Soto, F., Itzhak, D., McCarthy, F., Wichmann, C., Steger, M., Ohmayer, U., Distler, U., Kaspar-Schoenefeld, S. and Prianichnikov, N., 2021. MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nature Biotechnology, pp.1-11.