mokapot -- Semi-Supervised PSM Confidence Estimation

AlphaPept — Python-based, open-source proteomics pipeline for DDA mass spectrometry data analysis. Provides feature detection, peptide identification via database search, deep learning-based scoring,

3 shared topics • 1 shared operation

Comet — open-source tandem mass spectrometry (MS/MS) sequence database search engine for peptide identification. Searches MS/MS spectra against FASTA protein databases producing pepXML, mzIdentML, SQT

2 shared topics • 1 shared operation

DIA-NN (Data-Independent Acquisition by Neural Networks) is a universal software suite for DIA proteomics data analysis. Processes raw mass spectrometry files (.mzML, .raw, .d, .wiff) using neural net

2 shared topics • 1 shared operation

MaxQuant — quantitative proteomics platform for analyzing large-scale mass spectrometry data. Integrates the Andromeda search engine for peptide identification, supports label-free quantification (LFQ

2 shared topics • 1 shared operation

PyTorch Geometric (PyG) — graph neural network library built on PyTorch for learning on graphs and irregular structures. Provides message-passing layers (GCN, GAT, GraphSAGE, GIN, Transformer), mini-b

2 shared topics • 1 shared operation