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OpenMS
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Peptide Identification with MSFragger.
pot. predecessor tools | → MSFraggerAdapter → | pot. successor tools |
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any signal-/preprocessing tool (in mzML format) | IDFilter or any protein/peptide processing tool |
MSFragger must be installed before this adapter can be used. This adapter is fully compatible with version 3.2 of MSFragger and later versions of MSFragger were tested up to version 3.5.
All MSFragger parameters (as specified in the fragger.params file) have been transcribed to parameters of this OpenMS util. It is not possible to provide an explicit fragger.params file to avoid redundancy with the ini file. This adapter creates an fragger.params file prior to calling MSFragger. If the fragger.params file should be inspected, set the -debug option to 2. MSFraggerAdapter will print the path to the working directory to standard out.
MSFragger can process multiple input files (mzML, mzXML) one after another. The number of output files specified must match the number of input spectra files. The output file is then matched to the input file by index. The default parameters of the adapter are the same as given by the official MSFragger manual.
Please cite: Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu & Alexey I Nesvizhskii MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Nature Methods volume 14, pages 513–520 (2017) doi:10.1038/nmeth.4256
The command line parameters of this tool are:
INI file documentation of this tool: