directLFQ

directLFQ is an open-source Python package for quantifying protein intensities based on peptide intensities or fragment-ion intensities measured with from Mass Spectrometry-based proteomics. It preserves peptide ratios, shows very accurate quantification and has a robust normalization approach. Furthermore, it allows fast processing also of very large sample cohorts, as runtime increases linearly with sample number. It is part of the AlphaPept ecosystem from the Mann Labs at the Max Planck Institute of Biochemistry and the University of Copenhagen.

You can process DIA and DDA data analyzed by AlphaPept, MaxQuant, FragPipe, Spectronaut and DIANN as well as generic formats, using a Graphical User Interface (GUI) or the python package.

• directLFQ
  • About
  • Installation
  • One-click GUI
  • Pip
  • Developer
  • Running directLFQ
  • GUI
  • CLI
  • Python and Jupyter notebooks
  • Troubleshooting
  • Citations
  • How to contribute
  • License
  • directLFQ commands
  • directLFQ output
  • preparing input files
  • Spectronaut
  • DIA-NN
  • MaxQuant
  • FragPipe
  • generic input format
  • reproducing data analyses from the paper

About

Generating protein intensities from Mass Spectrometry proteomics data comes with a variety of challenges. Differing peptides that belong to the same protein can have strongly differing intensities, for example due to differing ionization efficiencies. Missing values (i.e. peptides that have been detected in one run but not in the other) make simple summarization of peptide intensities to protein intensities problematic. Differences in sample loading can introduce systematic biases into the analysis. With directLFQ, we provide a novel algorithm for addressing these challenges in an efficient and accurate manner. directLFQ retains peptide ratios and uses them to infer protein ratios and uses the concept of intensity traces for it's main processing steps. For futher details on the algorithm, please refer to the preprint.

Installation

directLFQ can be installed and used on all major operating systems (Windows, macOS and Linux). There are currently two different types of installation possible:

• One-click GUI installer: Choose this installation if you only want the GUI and/or keep things as simple as possible.