The need for new and updated computational tools for proteomics never ceases, as the instrumentation and experimental methodology for data generation continue to evolve. A new biennial series carried out by Journal of Proteome Research will make it easier to find and select new tools in proteomics and related domains.
In the first Special Issue dedicated to this cause, you will find a full list of software tools, web applications, databases for data analysis, and visualization that are user-friendly, easily adaptable, and have broad applicability in proteomics workflow and merit wide dissemination.
According to the editorial written by the guest editors of this Special Issue, “The described tools cover a range of applications and topics that are useful in different stages in a data analysis workflow, from working with raw mass spectrometry data and evaluating data quality to visualizing protein interaction networks as an endpoint of an analysis. The diversity of the tools spans quantifying proteins to analyzing post-translational modifications and expanding analyses into metabolomics or transcriptomics. Some are web-based, whereas others have custom graphical user interfaces or are collections of R or Python functions for use in R or Python scripts, respectively. This diversity underscores the versatility of software tools available in proteomics and permits the selection of the best fit based on, for example, user expertise or analysis platform.”