手把手教你 MaxQuant LFQ 蛋白搜库定量：从 RAW 到表达矩阵（PXD020248）

TL;DR - A practical MaxQuant workflow for converting PXD020248 mass-spectrometry RAW files into an LFQ protein-expression matrix. It outlines data preparation, experimental design, database selection, and search parameters, but stops before showing the actual run and results.

• The full dataset contains 24 RAW files: 2 treatments × 6 biological replicates × 2 fractions; the tutorial’s reduced example uses 12 files.
• It uses a reviewed human SwissProt FASTA plus MaxQuant’s built-in contaminant database.
• Key settings include Trypsin/P digestion, 1% PSM/protein FDR, LFQ, unique-peptide quantification, and match-between-runs.
• The resulting proteinGroups.txt LFQ intensity columns are intended as input for downstream differential analysis.