It groups top-down spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. TopPIC Top-down mass spectrometry based Proteoform Identification and Characterization identifies and characterizes proteoforms at the proteome level by searching top-down tandem mass spectra against a protein sequence database. It efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications PTMs , accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score MIScore , to increase the speed, sensitivity, and accuracy. TopMG Top-down mass spectrometry based proteoform identification using Mass Graphs is a software tool for identifying ultra-modified proteoforms by searching top-down tandem mass spectra against a protein sequence database. It is capable of identifying proteoforms with multiple variable PTMs and unexpected alterations, such as histone proteoforms and phosphorylated ones.
TopFD Top-down mass spectral Feature Detection is a software tool for top-down spectral deconvolution, which groups top-down mass spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from MS1 spectra. Raw mass spectral data generated from various mass spectrometers can be converted to mzML or mzXML files using msconvert. In addition, TopFD creates two folders containing java scripts files of spectral data for spectral visualization and other files generated in spectral deconvolution. For example, when the input file name is spectra.
GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together. Work fast with our official CLI. Learn more. If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again. If nothing happens, download the GitHub extension for Visual Studio and try again. On some Linux distributions, you might meet the problem "Could not loading a transcoding service". To fix this, please add following lines into your. MSYS2 is used for Windows building. Please follow the instructions from here.
Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database. Contact: xwliu iupui. Supplementary information: Supplementary data are available at Bioinformatics online.