Ecosystem

The alphapept ecosystem aims to provide open source tools for every step of analysis of data generated by modern proteomics workflow. Developed tools cover, for example io operations, providing fundamental data structures, search, quantification, biological interpretation, the visualization of raw data and processed data.

Packages in the alphapept ecosystem must adhere to stringent standards that aim to assure quality of the analysis. This includes

• Comprehensive tests of all functionalities, especially key algorithmic steps
• A user-friendly documentation with tutorials and recommendations on the usage
• A streamlined installation

Available packages

Explore available packages, and checkout installation instructions, tutorials, and the respective publications

alphaDIA

An open search engine for data-independent acquisition (DIA) experiments

alphapept

An open search engine for data-dependent acquisition (DDA) experiments

directLFQ

Label-free quantification for accurate protein abundance measurements

alphaquant

Accurate and sensitive peptide and protein quantification with trees

alphapeptstats

Downstream analysis of mass-spectrometry-based proteomics data

alphabase

Fundamental infrastructure for the handling of proteomics data

alphapeptdeep

Modular Deep learning for shotgun proteomics

alpharaw

Unified, vendor-agnostic access and and storage of raw MS data

alphatims

Access and visualize LC-TIMS-Q-TOF data

alphakraken

A fully automated data processing and analysis system for mass spectrometry experiments.

dvp-io

Read and write funtionalities for deep visual proteomics data

pydiaid

Automated Isolation Design for dia-PASEF methods

alphaviz

Browser-based interactive visualization of processed mass spectrometry data from Bruker instruments

alphamap

Visual annotation of proteomics data with sequence specific knowledge