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Computed Values

Reference for all output columns produced by mokume's quantification methods.

Quantification Columns

Column Method Description
PiBAQ piBAQ Per-protein piBAQ after shared-peptide signal is allocated proportionally or, without anchor signal, equally.
PiBAQNorm piBAQ PiBAQ / sum(PiBAQ) per sample
PiBAQLog piBAQ 10 + log10(PiBAQNorm)
PiBAQPpb piBAQ PiBAQNorm * 100,000,000 (parts per billion)
PiBAQBec piBAQ + ComBat Batch effect corrected piBAQ
FamilyId piBAQ Canonical accession identifying the protein family used by the piBAQ algorithm
FamilySize piBAQ Number of canonical members in the family (1 = singleton, isolated protein)
EvidenceLevel piBAQ high (all members meet the high-anchor threshold), medium (at least one member meets the minimum), or family_only (none does)
TopNIntensity TopN Average of top N peptides (e.g., Top3Intensity, Top5Intensity)
MaxLFQIntensity MaxLFQ MaxLFQ algorithm result
DirectLFQIntensity DirectLFQ DirectLFQ intensity traces
SumIntensity Sum Sum of all peptide intensities
Intensity Unified pipeline Standard output column (all methods)

Derived Values (piBAQ)

Column Formula Description
TPA NormIntensity / MolecularWeight Total Protein Approach
CopyNumber ProteomicRuler calculation Protein copies per cell
Concentration[nM] ProteomicRuler calculation Protein concentration

Metadata Columns

Column Description
ProteinName UniProt accession (e.g., P02452)
SampleID Sample identifier
Condition Experimental condition
BioReplicate Biological replicate
PeptideSequence Amino acid sequence
NormIntensity Normalized peptide intensity

Differential Expression Columns

The kernel writes one DE result CSV per contrast. The leading columns are shared across methods; later columns are method-specific (e.g. t_stat/AveExpr/B for limma, sca_t/peptide_count for deqms, d_stat for rots).

Column Description
ProteinName UniProt accession (same header for single-method and ensemble output)
log2FC Log2 fold change between conditions
pvalue Raw p-value
adj_pvalue FDR-adjusted p-value
log_pvalue Natural logarithm of the raw p-value (DEqMS only; remains finite when pvalue underflows to zero)
significance Whether the protein passes the --de-log2fc / --de-fdr thresholds

Pipeline Output Format

All quantification methods in the unified pipeline (features2proteins) produce a wide-format output: rows are proteins, columns are samples.

ProteinName,sample1,sample2,sample3,...
P02452,1234.5,5678.9,2345.6,...
P12345,9876.5,4321.0,8765.4,...

For ratio quantification, values are in log2 space (log2 sample/reference).