![]() It is available freely for academic research, non-commercial or educational purposes under academic license. The entire MSFragger suite of tools (MSFragger-Core, MSFragger-LOS, MSFragger-Glyco, MSFragger-DIA, MSFragger-Labile), collectively known as “MSFragger”, is distributed as a single JAR file. If you see an error saying cannot find Bruker native library, please try to install the Visual C++ redistibutable. Please note: timsTOF data requires Visual C++ Redistributable for Visual Studio 2017 in Windows. Thermo RAW - Thermo raw files (.raw) can be read directly, conversion to mzML is not requiredīruker timsTOF PASEF - MSFragger can read Bruker timsTOF PASEF (DDA) raw files (.d) directly, as well as MGF files converted by the Bruker DataAnalysis program. MzML/mzXML - data from any instrument in mzML/mzXML format can be used The following spectral file formats can be searched directly with MSFragger, see the FragPipe homepage for compatibility with workflow components downstream from MSFragger. Example parameter files can be found here. See the complete documentation, including a list of Frequently Asked Questions. MSFragger writes peptide-spectrum matches in either tabular or pepXML formats, making it fully compatible with downstream data analysis pipelines such as Trans-Proteomic Pipeline and Philosopher. As a standalone Java executable, which we recommend using with Philosopher pipeline.MSFragger is implemented in the cross-platform Java programming language and can be used three different ways: ![]() MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides, and glycopeptide identification (N-linked and O-linked). It has demonstrated excellent performance across a wide range of datasets and applications. MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. ![]()
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