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data-import

separate

Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted -- removes decoys (REV__/Reverse), contaminants (CON__/Potential contaminant), Only-identified-by-site groups, and resolves semicolon razor/leading protein-ID ambiguity in MaxQuant proteinGroups.txt, DIA-NN report.parquet, and mzML/mzXML. Distinguishes Intensity (raw) vs LFQ intensity (MaxLFQ) vs iBAQ, treats a MaxQuant zero as missing (NaN, not log2(-inf)), and inherits the acquisition mode's missingness contract (DDA MNAR vs DIA MCAR). Use when starting an analysis from raw spectra or a search engine output. Downstream normalization and stats are differential-abundance; reporter-ion/MaxLFQ quant is quantification; protein grouping is protein-inference.

When to use

• Loading mass-spectrometry data into Python/R
• Stripping decoy and contaminant rows
• Resolving semicolon razor/leading protein-ID ambiguity
• Distinguishing Intensity vs LFQ intensity vs iBAQ
• Treating MaxQuant zero as missing (NaN)
• Inheriting acquisition mode missingness contract (DDA MNAR vs DIA MCAR)
• Reading raw spectra or search engine outputs

When not to use

• Downstream normalization and stats
• Reporter-ion/MaxLFQ quant computation
• Protein grouping/inference
• Format conversion (RAW -> mzML)
• Peptide-identification
• Statistical testing
• Batch correction
• Actual imputation step

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