MSstats — Bioconductor R package for statistical analysis of quantitative mass spectrometry-based proteomics experiments. Supports label-free DDA, TMT, iTRAQ, SRM/MRM, and DIA workflows. Provides prep
Use with AI
Install the MCP server or CLI to instantly fetch MSstats documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/msstats
MaxQuant — quantitative proteomics platform for analyzing large-scale mass spectrometry data. Integrates the Andromeda search engine for peptide identification, supports label-free quantification (LFQ
3 shared topics • 1 shared operation
Philosopher — fast, scalable Go toolkit for shotgun proteomics data analysis. Provides database downloading, peptide validation (PeptideProphet), protein inference (ProteinProphet), PTM localization (
3 shared topics • 1 shared operation
Use when working with sage — sage — ultrafast Rust proteomics search
3 shared topics • 1 shared operation
Spectronaut -- commercial DIA (Data-Independent Acquisition) proteomics software from Biognosys for analyzing DIA-MS data. Supports library-based and library-free (directDIA / Pulsar) peptide-centric
3 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 • 2 shared operations