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Proteome Discoverer — Thermo Fisher Scientific's integrated proteomics software platform for mass spectrometry data analysis. Provides SEQUEST HT and Mascot database searching, Percolator PSM validati
Use with AI
Install the MCP server or CLI to instantly fetch Proteome Discoverer documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/proteome-discoverer
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
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
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
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