Welcome to msproteomicstools’s documentation!

msproteomicstools is a Python library that can be used in LC-MS/MS based proteomics. It features a core library called msproteomicstoolslib and several associated executable scripts that use the library as well as a GUI for visualizing chromatograms, specifically output from OpenSWATH.

For questions, bug reports and contributions, please visit the official GitHub page.

Contents of the library:

• Algorithms
  • Algorithms - Alignment
  • Algorithms - Graphs
• Math
  • Smoothing Module
  • LinearRegression Module
  • Chauvenet Module
• DataStructures - Alignment
  • Run Module
  • PrecursorGroup Module
  • Precursor Module
  • PeakGroup Module
• DataStructures - Basic
  • Aminoacides Module
  • Modifications Module
  • Peak Module
  • Peptide Module
  • Residues Module
  • DDB Module
• Format
  • Transformation Collection Module
  • File Reader Module
  • Data Matrix Module
  • Spectral library Module
• Optimized Cython
  • Peakgroup (optimized)
  • Precursor (optimized)
  • PrecursorGroup (optimized)
  • CyLinearInterpolateWrapper (optimized)
  • CyLightTransformationData (optimized)
  • DataCacher (optimized)
  • MST Algorithm (optimized)

Contents of the GUI code:

• TAPIR GUI executable
  • TAPIR Main Window
  • TAPIR ApplicationView (central window)
  • TAPIR Widgets
• TAPIR Models and Views
  • OpenSWATH - GUI Models
    • MSData Data model Module
    • TreeModels Module
    • SWATH MS Run Module
    • ChromatogramTransition Module
  • OpenSWATH - GUI Views
    • PeptideTreeView Module
    • Plot Module

Contents of the executables:

• Alignment executables
  • FeatureAlignment executable
  • FeatureAlignment Module
  • Noise imputation Module

Indices and tables

• Index
• Module Index
• Search Page