![]() 3 1.0 – Installation and Hardware Requirements. The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Unit, Department of Biomedicine, University of Bergen, Bergen, Norway Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany Vaudel et al.: PeptideShaker - Supplementary Material Note: Version as accepted after peer review. Neurology, Haukeland University Hospital, Bergen, Norway 6ĭepartment of Medical Protein Research, VIB, Ghent, Belgiumĭepartment of Biochemistry, Ghent University, Ghent, Belgiumīiology Unit, University of Bergen, Norway The Norwegian Multiple Sclerosis Competence Centre, Department of KG Jebsen Centre for MS-research, Department of Clinical Medicine, Of Clinical Medicine, University of Bergen, Bergen, Norway Unit, Department of Biomedicine, University of Bergen, Bergen, Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Berven2,4,5, Albert Sickmann1, Lennart Martens6,7,* and Harald Barsnes2,8 PeptideShaker: Completing the proteomics data cycle Marc Vaudel1,2, Julia M. To add custom reports see Export > Identification Features > Reports in PeptideShaker.Vaudel et al.: PeptideShaker: Completing the proteomics data cycle. gzip Indicates whether the report should be compressed. documentation Comma separated list of types of report documentation to export. report_prefix Prefix added to the report file name. reports Comma separated list of types of report to export.Ĥ: Default PSM Report with non-validated matches,ĥ: Default Peptide Phosphorylation Report,ħ: Default Peptide Report with non-validated matches,Ĩ: Default Protein Phosphorylation Report,ġ0: Default Protein Report with non-validated matches, In distributed setups, we recommend keeping a clean copy of PeptideShaker, and distribute it to the different nodes prior to execution. ![]() It is recommended to use a single instance of PeptideShakerCLI at a time. Temporary folders used in the processing can be set via PathSettingsCLI. Alternatively, the parameters can be passed directly to PeptideShakerCLI by using the command line arguments of the IdentificationParametersCLI. ![]() Identification parameter files are in the json format and can be created in the graphical user interface, using the IdentificationParametersCLI, or using third party tools. Identification parameters can be provided as a file. Note that ReportCLI, FollowUpCLI, MzidCLI and PathSettingsCLI options can also be appended directly to PeptideShakerCLI command lines.Īll command line options have the same overall structure and only differ in the features and parameters available.
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