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proteomics-pipeline

separate

Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein abundance with limma/DEqMS/MSstats. Use when committing the search database + acquisition mode (DDA vs DIA) up front, re-controlling FDR at PSM AND peptide AND protein-group level (not just PSM), removing contaminant/reverse rows and inspecting RAW distributions before normalizing, bridging cross-plex TMT with an IRS reference channel, modeling MNAR missingness rather than downshift-imputing on/off proteins, batching as a covariate (not pre-subtracted), and testing with treat()/DEqMS. Hands mechanism to the proteomics component skills; not a re-teach of any single step.

When to use

• bottom-up proteomics orchestration
• differential protein abundance
• MaxQuant/FragPipe/DIA-NN output processing
• FDR control at PSM, peptide, and protein-group levels
• MNAR missingness modeling
• cross-plex TMT bridging with IRS
• batch covariate modeling
• treat() and DEqMS testing

When not to use

• re-teaching single step internals
• blind deletion of contaminant rows
• downshift imputation for on/off proteins
• pre-subtracting batch effects
• reporting MBR-filled counts as directly measured

Skill page

Source