BMC Bioinf 12:70īarsnes H, Eidhammer I, Martens L (2011) A global analysis of peptide fragmentation variability. Proteomics 14:1001–1005īarsnes H, Vaudel M, Colaert N et al (2011) Compomics-utilities: an open-source Java library for computational proteomics. Vaudel M, Venne AS, Berven FS et al (2014) Shedding light on black boxes in protein identification. Vizcaino JA, Deutsch EW, Wang R et al (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Vizcaino JA, Cote RG, Csordas A et al (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Vaudel M, Barsnes H, Berven FS et al (2011) SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics Clin Appl 3:18–29Ĭox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Vizcaino JA, Mueller M, Hermjakob H et al (2009) Charting online OMICS resources: a navigational chart for clinical researchers. Mol Cell Proteomics 11:3–14īarsnes H, Martens L (2013) Crowdsourcing in proteomics: public resources lead to better experiments. Expert Rev Proteomics 9:519–532Ĭhalkley RJ, Clauser KR (2012) Modification site localization scoring: strategies and performance. Vaudel M, Sickmann A, Martens L (2012) Current methods for global proteome identification. Proteomics 11:2105–2114Įlias JE, Gygi SP (2010) Target-decoy search strategy for mass spectrometry-based proteomics. Vaudel M, Burkhart JM, Sickmann A et al (2011) Peptide identification quality control. ![]() Nesvizhskii AI (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data: the protein inference problem. Nature 422:198–207ĭuncan MW, Aebersold R, Caprioli RM (2010) The pros and cons of peptide-centric proteomics. If you get problems running PepNovo+ on Linux (or OSX), please try the following: (1) install dos2unix, (2) run the following two commands inside the resources/PepNovo folder: dos2unix Models/*.* and dos2unix Models/*/*.*.įor problems related to Java, memory or startup issues, please see: Java Troubleshooting.įor other questions or suggestions please contact the developers of DeNovoGUI by setting up an Issue with your comment, or by sending an e-mail to the DeNovoGUI Google Group.Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Note that PepNovo+ is not supported on Linux 32 bit, pNovo+ is only supported on Windows, and that DirectTag is currently not supported on Mac (support is in development). ![]() We welcome bug reports, suggestions of improvements, and contributions via our issue tracker. We apologize for any inconvenience and will try to fix things to the best of our capabilities. Issue Trackerĭespite our efforts at enforcing good practices in our work, like every software, DeNovoGUI might crash, fail to cover specific use cases, not perform as well as expected. Issues, Questions and Bug Reports Code of ConductĪs part of our efforts toward delivering open and inclusive science, we follow the Contributor Convenant Code of Conduct for Open Source Projects. No additional installation required!ĭeNovoGUI can also be used via the command line, see DeNovoCLI for details. To start using DeNovoGUI, unzip the downloaded file, and double-click the DeNovoGUI-X.Y.Z.jar file. If you use DeNovoGUI as part of a publication, please include this reference.ĭeNovoGUI provides a user-friendly open-source graphical user interface for running the de novo sequencing algorithms Novor, DirecTag, PepNovo+ and pNovo+ (beta) on Windows, Mac and Linux.Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H: DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.
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