About WinProphet

    WinProphet is a Windows-based software tool with graphical interfaces for users to creat, edit, manage, and execute proteomics pipelines based on Trans-Proteomic Pipelines (TPP). 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 quantitations. The constructed pipelines can be exported as XML files with all of the parameter settings for reusability and portability. The tool is standalone and installation-free. We have constructed five sample pipelines of varying purposes to showcase its capability. Users can build up customized pipelines from scratch or use these samples as templates with minimum revision to accommodate the input files and parameters for proteomics data analysis.

Software Download:

WinProphet (download here)

User Guide and Datasets for Sample Pipelines

  • User guide for setup and running WinProphet (pdf)
  • Pipeline 1: Protein identification for Erwinia sample (rar)
  • Pipeline 2: Protein identification and iTRAQ-8 quantitation for Human A549 cell lysate dataset (rar)
  • Pipeline 3: Protein identification and label-free quantitation for MCF-7 breast cancer cell line dataset (rar)
  • Pipeline 4: DIA data analysis for Human HeLa cell lysate dataset (rar)
  • Pipeline 5: Spectral library construction and search for Erwinia sample (rar)

Important Notices

The recommended system environment is:
  1. Operating System:  Windows 7, 8, 10, and Windows Server 2018, 2012
  2. CPU:  Intel CPU 1.8 GHz or faster
  3. HDD:  depending on the raw data file size. It is recommended the free space on the disk is several times of the size of the raw data files
  4. Memory:  depending on the input file size. In general, a minimum of 4GB is suggested
  5. Microsoft .Net Framework: the version of 4.0 or higher is required


Chen et al., “WinProphet: a user-friendly pipeline management system for proteomics data analysis based on Trans-Proteomic Pipeline".
Analytical Chemistry, 2019.

Update Information

2019.06.29 V1.1.1 is available for download.
  • A bug fix which disables adding file name to Pipeline Editor when the file path consists of spaces.
  • Automatic copy of directory name from the previous operation after users select function.
  • A message box to notify users General Mode of Comet and XTandem panel is only for setting parameters. The saved parameters can only be inspected from Expert Mode.
  • A dialog box which allows users to resume the pipeline after it is interrupted due to error.
  • Unifying the font used in the Expert Mode of Comet and XTandem's parameter setting panel.
2019.05.07 V1.0.6 is available for download.
  • A bug fix for file browser.
  • User interface enhancement for multiple input files.
2019.04.25 V1.0.5 is available for download.
  • A bug fix of program error when selecting intput files.
  • A newly added button for creating empty operation.
  • A message box to allow users to apply the selected directory to all the operations.
  • Disabling database file textbox in the expert mode of comet parameter panel.
  • Showing the saved parameter file name for users to inspect the parameters in Expert Mode.
2018.09.15 V1.0.0 is available for download.
  • WinProphet version 1.0.0 is officially on-line.
2018.05.04 V0.0.0 is available for download (TESTING).
  • WinProphet beta version is officially on-line.