mspypeline is a package for analysing mass spectrometry-based proteomics data.
The source code is available on github.
mspypeline was developed for the analysis of proteomic data generated by MaxQuant to provide a
tool to analyze complex datasets in a standardized manner with minimal effort and to eliminate the chance of human
error or obscuring variability during data analysis.Designed with an intuitive and concise graphical user interface (GUI),
mspypeline offers researchers,
unfamiliar with programming or data analysis, the opportunity to explore and visualize their data independently and in
a time-effective manner. A structured workflow (see figure to the right) can be followed to perform a comprehensive and
conclusive analysis that starts with quality control of the data, followed by the assessment and choice of
data preprocessing operations to finally allow optimal exploratory analysis. By automizing the calculations and the
generation of versatile figures, mspypeline supports data analysis within minutes.
Simultaneously, the more experienced user may interact closer with the mspypeline package to perform advanced
analysis exploiting the plethora of customization options.Standardization and reproducibility of the analysis are ensured by the automated logging of all analysis settings and
saving them to a separate configuration file.
Thus,
mspypeline provides a platform that supports users in their proteomics data analysis generated by mass spectrometry
by giving insight into the data, offering parameter adaptation when needed, generating custom figures and performing
differential expression analysis and hypothesis testing to reach biologically relevant conclusions.Please refer to the other parts of the documentation for :ref:`installation <installation>`,
:ref:`how to get started <get-started>`, or use the search.
.. toctree:: :maxdepth: 2 :caption: Contents installation get_started workflow file_readers analysis_options settings_and_configuration package_config examples gallery examplary_bio_analysis API <api_reference/index>