MSstatsTMT

MSstatsTMT provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.

Key Features:

• Data visualization: The package includes functionality for visualizing proteomics data.
• Protein quantification and normalization: The package performs protein quantification and normalization for TMT-labeled proteomic data.
• Statistical modeling and inference: The package provides statistical modeling and inference for detecting differentially abundant proteins.
• Interoperability: The package is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Scientific Applications:

• Differential abundance analysis: MSstatsTMT enables detection of differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.

Methodology:

The package provides statistical modeling and inference for protein significance analysis in TMT-labeled proteomic experiments.