The Proteomics group at the Walter & Eliza Hall Institute of Medical Research (WEHI) continue to develop and provide free software to the Australian Proteomics community. The software tools and packages are available from http://www.wehi.edu.au/people/andrew-webb/1295/andrew-webb-resources. Originally software tools were aimed principally at Mascot users due to the popularity of the Mascot search engine accessed through the Australian Proteomics Computationally Facility (APCF). This resource is still provided freely to academic researchers in Australia even though it is no longer grant funded. Additional software and resources such as “Download tools”, “Sequence Databases” as well as “contaminants” are updated periodically. More recently software was developed for converting “MaxQuant” peaklists (APL) to generic peaklists (MGF) for usage in current and legacy software (e.g. denovo sequencing). A newly developed multi-threaded “MascotParser” is available which provides an easily configurable output format that is not available in the current download options. The latest most exciting software tool is MSCypher which brings together multiple freely available software programs such as alternative search engines (Digger, Comet, MSGFplus, Andromeda etc.) plus retention time prediction (Elude), machine learning tools (Random Forest) and the ability to automatically run R scripts such as Limma/Voom and/or MSstats. The MSCypher workflow is entirely user configured and command line. A graphical user interface, cloud-based access, open-mass searches are under development. Support for the PEFF sequence database format will also become available to better support variants, mutations and SNPs.