ProteoTorch

A Python package for deep learning and fast machine learning analysis of MS/MS database search results.

Key Features

ProteoTorch accepts as input a Percolator INput (PIN) file containing target/decoy PSM features. By default, several iterations of deep semi-supervised learning are then performed to classify target and decoy PSMs, and the output PSM scores are recalibrated using the resulting learned parameters.

ProteoTorch provides the following semi-supervised machine learning classifiers:

Additional Features

ProteoTorch provides an ultrafast q-value library (heavily optimized for Python), plotting tools to benchmark/compare MS/MS post-processor results, and an easy-to-use Python API for the MS/MS semi-supervised learning algorithm (with cross-validation) originally implemented in the C++ package Percolator.