CLI Reference

mokume provides six main commands. In practice, most users start with features2proteins for quantification workflows or tissuemap for tissue atlas workflows. Use mokume --help or mokume <command> --help for details.

features2proteins

The unified pipeline: features to protein quantification in one step.

mokume features2proteins [OPTIONS]

Required Options

Option	Description
-p/--parquet	Input parquet file (quantms.io/qpx format)
-o/--output	Output protein intensities CSV

Input & Filtering

Option	Default	Description
-s/--sdrf	none	SDRF file for sample metadata
--min-aa	7	Minimum amino acid length
--min-unique	2	Minimum unique peptides per protein
--remove-contaminants	on	Remove contaminants and decoys
--keep-contaminants	off	Keep contaminants and decoys

Quantification

Option	Default	Description
--quant-method	maxlfq	Method: maxlfq, directlfq, ibaq, topn, sum, median, ratio
--fasta	none	FASTA file (required for iBAQ)
--topn	3	N for TopN quantification
--ion-alignment	none	Ion alignment: none or hierarchical
--directlfq-cores	auto	CPU cores for DirectLFQ
--directlfq-min-nonan	1	Min non-NaN values for DirectLFQ

Normalization

Option	Default	Description
--run-normalization	median	Run-level: median, mean, max, global, max_min, iqr, none
--sample-normalization	globalMedian	Sample-level: globalMedian, conditionMedian, hierarchical, tmm, none
--normalization-proteins	none	File with protein IDs for normalization

IRS (Multi-Plex TMT)

Option	Default	Description
--irs	off	Enable IRS normalization
--irs-reference-samples	auto	Comma-separated reference sample names
--irs-sdrf-column	auto	SDRF column for reference detection
--irs-sdrf-values	auto	Values indicating reference samples
--irs-reference-regex	pool\|powder\|ref\|reference\|bridge	Regex for reference auto-detection
--irs-stat	median	Plex reference statistic: median or mean
--irs-remove-reference	off	Remove reference samples from output

Coverage Filter

Option	Default	Description
--coverage-threshold	none	Min fraction of non-missing values per condition

Ratio Quantification

Option	Default	Description
--ratio-fraction-merge	mean	Fraction merge strategy: mean or max

Batch Correction

Option	Default	Description
--batch-correction	off	Enable ComBat batch correction
--batch-method	sample_prefix	Detection method: sample_prefix, run, column
--batch-column	none	SDRF column used when --batch-method=column
--batch-covariates	none	Comma-separated SDRF columns to preserve
--batch-parametric / --batch-nonparametric	parametric	ComBat estimation mode
--batch-mean-only	off	Only adjust batch means
--batch-ref	none	Reference batch ID

Differential Expression

Option	Default	Description
--de	off	Enable differential expression analysis
--de-contrasts	—	Comma-separated contrasts (e.g., "A vs B,A vs C")
--de-contrasts-file	—	TSV file with columns group1, group2
--de-method	auto	Method: auto, limrots, deqms, or proda
--de-log2fc	0.5	Minimum absolute log2 fold change
--de-fdr	0.05	Maximum FDR threshold
--de-fdr-method	bh	FDR correction: bh or ihw
--de-output	auto	Output file for DE results

Contrasts must be explicitly provided via --de-contrasts and/or --de-contrasts-file. Both can be combined.

--de-method auto selects deqms for directlfq quantification and limrots for other quantification methods.

Plots & Reports

Option	Default	Description
--plot-dir	none	Output directory for plots
--plot-volcano	off	Generate volcano plots
--plot-heatmap	off	Generate per-contrast DE heatmaps (top 50 by |log2FC|)
--plot-pca	off	Generate PCA plots
--highlight-genes	none	Comma-separated gene names to highlight
--interactive-report	off	Generate interactive HTML QC report
--report-output	auto	Output path for HTML report

Export

Option	Default	Description
--export-peptides	none	Export normalized peptides to file
--export-ions	none	Export normalized ions (DirectLFQ only)

---

features2peptides

Feature-level to peptide-level normalization.

mokume features2peptides [OPTIONS]

Core Options

Option	Default	Description
-p/--parquet	required	Input parquet file
-s/--sdrf	none	SDRF file for metadata
-o/--output	required	Output peptide intensity file
--min_aa	7	Minimum amino acid length
--min_unique	2	Minimum unique peptides per protein
--remove_ids	none	File with protein IDs to exclude
--remove_decoy_contaminants	off	Remove decoys and contaminants
--remove_low_frequency_peptides	off	Remove peptides in <20% of samples

Normalization

Option	Default	Description
--run-normalization	median	Feature normalization: median, mean, max, global, max_min, iqr, none
--sample-normalization	globalMedian	Sample normalization: globalMedian, conditionMedian, hierarchical, tmm, none
--skip_normalization	off	Skip all normalization
--log2	off	Log2 transform output
--save_parquet	off	Save output as parquet

TMT / ITRAQ

Option	Default	Description
--irs_channel	none	Explicit pooled/reference channel label
--irs_autodetect_regex	none	Regex to detect pooled samples from SDRF
--irs_stat	median	IRS per-run statistic
--irs_scope	global	IRS scaling scope: global, by_mixture, or two_stage
--aggregation_level	sample	Aggregate at sample or run level

Filter Configuration

Option	Default	Description
--filter-config	none	YAML/JSON filter configuration file
--generate-filter-config	none	Generate example config and exit
--filter-min-intensity	none	Min intensity threshold (override)
--filter-cv-threshold	none	Max CV across replicates (override)
--filter-charge-states	none	Comma-separated charge states (override)
--filter-max-missed-cleavages	none	Max missed cleavages (override)
--filter-exclude-modifications	none	Comma-separated modifications (override)
--filter-min-unique-peptides	none	Min unique peptides (override)
--filter-min-features	none	Min features per run (override)
--filter-max-missing-rate	none	Max missing rate (override)

---

peptides2protein

Protein quantification from normalized peptide data.

mokume peptides2protein [OPTIONS]

Option	Default	Description
-p/--peptides	required	Input peptide intensity file
-f/--fasta	none	FASTA file (required for iBAQ)
--method	ibaq	Method: ibaq, top3, topn, maxlfq, sum, directlfq
-e/--enzyme	Trypsin	Enzyme for in-silico digestion
-n/--normalize	off	Normalize quantification values
--min_aa	7	Min amino acid length
--max_aa	30	Max amino acid length
-t/--tpa	off	Calculate TPA (iBAQ only)
-r/--ruler	off	ProteomicRuler (iBAQ only)
-i/--ploidy	2	Ploidy number
-m/--organism	human	Organism for histone data
-c/--cpc	200	Cellular protein concentration (g/L)
--topn_n	3	N for TopN quantification
--threads	-1	Threads for MaxLFQ (-1 = all cores)
--min_nonan	1	Min non-NaN for DirectLFQ
-o/--output	none	Output file path
--verbose	off	Print distribution info
--qc_report	QCprofile.pdf	QC report PDF path

Use --method topn --topn_n 5 or --method topn --topn_n 10 for Top5 or Top10-style quantification. -o/--output is effectively required for ibaq; for the other methods, omitting it prints the result table to stdout.

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correct-batches

Standalone batch correction for pre-quantified data.

mokume correct-batches [OPTIONS]

Option	Default	Description
-f/--folder	required	Folder with TSV files
-p/--pattern	*ibaq.tsv	File matching pattern
-o/--output	required	Output file path
-sid/--sample_id_column	SampleID	Sample ID column
-pid/--protein_id_column	ProteinName	Protein ID column
--ibaq_raw_column	IBAQ	Raw intensity column
--ibaq_corrected_column	IBAQ_BEC	Corrected intensity column
--comment	#	Comment character
--sep	\t	Field separator
--export_anndata	off	Export to AnnData h5ad

---

tissuemap

Per-dataset tissue proteome atlas analysis from QPX outputs.

mokume tissuemap [OPTIONS]

Option	Default	Description
--scan-dir	required unless --generate-config	Dataset directory or parent directory containing datasets
--output-dir	tissuemap_output	Output directory for results
--config	none	YAML configuration file
--generate-config	none	Generate a default YAML template and exit
--tmt-dataset	auto	Mark one or more dataset IDs as TMT
--n-jobs	8	Threads for dataset processing and embedding
--dpi	250	Plot resolution override

Note

Install the optional dependencies first with pip install mokume[tissuemap].

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tsne-visualization

t-SNE dimensionality reduction visualization.

mokume tsne-visualization [OPTIONS]

Option	Default	Description
-f/--folder	required	Folder with protein files
-o/--pattern	proteins.tsv	File matching pattern