Protein and peptide identifications are essential tasks in proteomics research and involve a series of steps in analyzing tandem mass spectrometry (MS/MS) data. Several software packages have been developed for such purpose, among which Trans-Proteomic Pipeline (TPP) is frequently used and supports various tools for different steps, e.g., database sequence search and statistical validation. TPP provides a web-based user interface named Pentunia to launch most of its functions. Despite its powerful functionality, TPP requires manual intervention to launch each step, including selecting tools and setting parameters. When a large number of MS/MS files need to be processed or the workflow is complicated, it is desirable to be free of manual effort. Thus, a software tool for pipeline creation and execution is in pressing need.
We have developed WinProphet, a tool to create and automatically execute a pipeline for proteomic analyses. It seamlessly integrates with TPP and other external command-line programs, supporting various functionalities including database search for protein and peptide identification, spectral library construction and search, DIA (Data-Independent Acquisition) data analysis, isobaric labeling and label-free quantitation. WinProphet is a standalone and installation-free tool with graphical interfaces for users to configure, manage, and automatically execute pipelines. The constructed pipelines can be exported as XML files with all of the parameter settings for reusability and portability. The executable files, user manual, and sample data sets of WinProphet are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_WinProphet.html.