Version Compatibility

Reference examples tested with: MSnbase 2.28+, ggplot2 3.5+, limma 3.58+, DEqMS 1.20+, ashr 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Proteomics Pipeline

"Process my proteomics data from raw MS files to differential abundance" → Orchestrate data import (pyopenms/MaxQuant), QC assessment, protein quantification, normalization, differential abundance testing (limma/DEqMS, or MSstats for feature-level designs), and PTM analysis.

Pipeline Overview