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Keywords:

  • MS;
  • Open-source freeware;
  • Protein identification;
  • Publication guidelines

MS-based proteomics is a bioinformatic-intensive field. Additionally, the instruments and instrument-related and analytic software are expensive. Some free Internet-based proteomics tools have gained wide usage, but there have not been any single bioinformatic framework that in an easy and intuitive way guided the user through the whole process from analyses to submission. Together, these factors may have limited the expansion of proteomics analyses, and also the secondary use (reanalyses) of proteomic data. Vaudel et al. (Proteomics 2014, 14, 1001–1005) are now describing their Compomics framework that guides the user through all the main steps, from the database generation, via the analyses and validation, and through the submission process to PRIDE, a proteomic data bank. Vaudel et al. partly base the framework on tools that they have developed themselves, and partly they are integrating other freeware tools into the workflow. One of the most interesting aspects with the Compomics framework is the possibility of extending MS-based proteomics outside the MS laboratory itself. With the Compomics framework, any laboratory can handle large amounts of proteomic data, thereby facilitating collaboration and in-depth data analyses. The described software also opens the potential for any laboratory to reanalyze data deposited in PRIDE.