Galaxy data processing interaction mass spectrometry visualization. The source code, additional documentation, and a fully functional demo is available at. Storage and processing of the data are performed via the versatile Galaxy platform (through SearchGUI, PeptideShaker, and moFF), while the interaction with the results happens via a locally installed web server, thus enabling researchers to process and interpret their own data without requiring advanced bioinformatics skills or direct access to compute-intensive infrastructures. Here we present PeptideShaker Online, a user-friendly web-based framework for the identification of mass spectrometry-based proteomics data, from raw file conversion to interactive visualization of the resulting data. A spectral library was generated by merging search results from three search engines (Mascot 18, XTandem 19 and MSGF+ 20) using PeptideShaker 21 and Skyline 22 (see Methods). A key element in simplifying this process is the development of interactive frameworks focusing on visualization that can greatly simplify both the interpretation of data and the generation of new knowledge. Also, PeptideShaker supports the creation of a well-annotated PRIDE XML file from the combined search result files from Mascot, OMSSA and XTandem. However, storing, processing, and interpreting these data can be a challenge. It also provides the jTraML library for the TraML standard file format. Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project.
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