shinyTANDEM

shinyTANDEM provides visualization, parameter management, and search automation for rTANDEM/X!Tandem MS/MS protein-identification results within the R/Bioconductor environment.

Key Features:

• Integration with rTANDEM and X!Tandem: Interfaces rTANDEM with the X!Tandem protein identification algorithm to process MS/MS data.
• Visualization of Results: Visualizes rTANDEM result objects and X!Tandem XML result files for interpretation of proteomic identifications.
• Parameter Management and Search Automation: Creates and manipulates parameter objects and automates searches, including multi-threaded analyses.
• Data Conversion Utilities: Converts search parameters and results between R objects and XML files.

Scientific Applications:

• MS/MS-based proteomic pipelines: Integrates rTANDEM/X!Tandem outputs into MS/MS-based proteomic analysis workflows in R/Bioconductor.
• Protein identification and high-throughput proteomics: Facilitates protein identification and high-throughput proteomics studies by enabling automated searches and result processing.

Methodology:

Interfaces rTANDEM to the X!Tandem algorithm; supports creation and manipulation of parameter objects; automates searches with multi-threaded processing; and converts parameters and results between R objects and XML files.