Comet

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,

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

DIA-NN R package — R toolkit for post-processing DIA-NN proteomics search results. Provides report loading (diann_load), precursor/peptide/protein matrix generation with FDR filtering (diann_matrix),

2 shared topics • 1 shared operation

FragPipe/MSFragger — ultrafast proteomics database search engine and computational pipeline for peptide identification from mass spectrometry (MS/MS) data. Supports closed search, open search for post

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