Computed Values
Reference for all output columns produced by mokume's quantification methods.
Quantification Columns
| Column |
Method |
Description |
Ibaq |
iBAQ |
Total intensity / theoretical peptide count |
IbaqNorm |
iBAQ |
ibaq / sum(ibaq) per sample |
IbaqLog |
iBAQ |
10 + log10(IbaqNorm) |
IbaqPpb |
iBAQ |
IbaqNorm * 100,000,000 (parts per billion) |
IbaqBec |
iBAQ + ComBat |
Batch effect corrected iBAQ |
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 (iBAQ)
| Column |
Formula |
Description |
TPA |
NormIntensity / MolecularWeight |
Total Protein Approach |
CopyNumber |
ProteomicRuler calculation |
Protein copies per cell |
Concentration[nM] |
ProteomicRuler calculation |
Protein concentration |
| 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
| Column |
Description |
log2FoldChange |
Log2 fold change between conditions |
pValue |
Raw p-value |
adjustedPValue |
FDR-adjusted p-value |
significant |
Whether the protein passes thresholds |
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).