Which function do I want?

Find your question in the left column. Each row is one verb of the bridge, the shared layer pyMzLib, mzLibRust and mzLibR all call, so the same table is also the name of the same function in Python, Rust and R. The wire verb links to its parameters, result fields, errors and caveats; the module heading links to the guide with worked examples.

This page is generated from the per-verb specs, so it cannot list a function that does not exist or miss one that does. A dash means that binding has not shipped the verb yet.

genes · guide

You want to	Python	Rust	R	Wire verb
Resolve every protein in the given databases to stable Ensembl gene ids, counted against a caller-supplied, release-pinned gene set, with one outcome per protein and the hash of every input.	pymzlib.proteins.resolve_genes	mzlib::proteins::resolve_genes_with	proteins_resolve_genes	genes resolve

isobaric · guide

You want to	Python	Rust	R	Wire verb
List the isobaric labelling kits mzLib can name, with every channel's label and reporter-ion m/z.	pymzlib.isobaric.kits	mzlib::isobaric::kits	isobaric_kits	isobaric kits

peptidoform · guide

You want to	Python	Rust	R	Wire verb
Convert full sequences from one notation to another with mzLib's sequence conversion service, one result per input: for example a MetaMorpheus full sequence to Unimod accessions.	pymzlib.peptidoform.convert	mzlib::peptidoform::convert_with	peptidoform_convert	peptidoform convert
Fetch a UniProt entry with its annotated modifications, digest it, and return every peptidoform with its fragment ions, plus a census of which annotations were applied.	pymzlib.peptidoform.fragments	mzlib::peptidoform::fragments_with	peptidoform_fragments	peptidoform fragments

pride · guide

You want to	Python	Rust	R	Wire verb
Download a PRIDE project's files, all of them or a selection, into a directory and report the paths written.	pymzlib.pride.download	mzlib::pride::download	pride_download	pride download
List a PRIDE Archive project's files as PRIDE's REST API publishes them, with every page already fetched: name, size, checksum, category and download locations.	pymzlib.pride.list_files	mzlib::pride::list_files_with	pride_list_files	pride files
List every file a PRIDE project holds by walking its FTP directory tree, subdirectories included, with approximate sizes.	pymzlib.pride.list_ftp_files	mzlib::pride::list_ftp_files_with	pride_list_ftp_files	pride ftp-files
Find PRIDE Archive projects by keyword, with every page fetched and no accession repeated: the discovery step that produces the accessions every other pride verb takes.	pymzlib.pride.search	mzlib::pride::search_with	pride_search	pride search

proteins · guide

You want to	Python	Rust	R	Wire verb
Annotate a stored MetaMorpheus protein-group table with Gene Ontology terms: one row per (group, term) that any member holds, directly or through an ancestor, with no member privileged.	pymzlib.proteins.annotate_go	mzlib::proteins::annotate_go_with	proteins_annotate_go	proteins annotate-go
Classify peptides as unique to one sequence, shared within a gene, shared across genes, or not in the databases, treating I and L as the same residue.	pymzlib.proteins.classify_peptides	mzlib::proteins::classify_peptides_with	proteins_classify_peptides	proteins classify-peptides
Read protein databases (UniProt XML or FASTA) into one row per protein, with GO terms and Ensembl gene links as long tables on request.	pymzlib.proteins.read	mzlib::proteins::read_with	proteins_read	proteins read
Download the current Gene Ontology release (go.obo) to a path, on purpose, keeping any different file already there as a timestamped backup.	pymzlib.proteins.update_go	mzlib::proteins::update_go	proteins_update_go	proteins update-go

quant · guide

You want to	Python	Rust	R	Wire verb
Quantify a search's peptides and proteins across mzML runs with FlashLFQ, returning per-run peptide and protein intensities and every chromatographic peak.	pymzlib.flashlfq.quantify	mzlib::flashlfq::quantify_with	flashlfq_quantify	quant flashlfq
Roll a FlashLFQ QuantifiedPeptides.tsv up to protein intensities per sample with FlashLFQ's median polish, under a new experimental design, without re-reading any spectra.	pymzlib.flashlfq.median_polish	mzlib::flashlfq::median_polish_with	flashlfq_median_polish	quant median-polish

readers · guide

You want to	Python	Rust	R	Wire verb
List every file type mzLib recognises, with the extension it dispatches on, the reader class that parses it, and the cross-format views it offers.	pymzlib.readers.formats	mzlib::readers::formats	readers_formats	readers formats
Say what kind of file a path is - the mzLib file type, its extension, its reader and the cross-format views it offers - without parsing its contents.	pymzlib.readers.identify	mzlib::readers::identify	readers_identify	readers identify
Read deconvolved MS1 features through the cross-format ms1_features view: m/z, charge, retention-time range, apex intensity and isotope count.	pymzlib.readers.read_features	mzlib::readers::read_features_with	readers_read_features	readers read-features
Read identifications through the cross-format spectral_match view - scan, sequences, accession, decoy flag, modifications and the q-value, rank and threshold a format records - optionally with each engine's scores as long rows.	pymzlib.readers.read_matches	mzlib::readers::read_matches_with	readers_read_matches	readers read-matches
Read the PTM site occupancy of a MetaMorpheus AllQuantifiedProteinGroups.tsv as one row per group, sample group, basis and modified site.	pymzlib.readers.read_occupancy	mzlib::readers::read_occupancy_with	readers_read_occupancy	readers read-occupancy
Read a MetaMorpheus AllQuantifiedProteinGroups.tsv as one row per protein group per sample group, with each sample group's spectral count and intensity as columns.	pymzlib.readers.read_protein_groups	mzlib::readers::read_protein_groups_with	readers_read_protein_groups	readers read-protein-groups
Read a FlashLFQ QuantifiedPeptides.tsv (or MetaMorpheus AllQuantifiedPeptides.tsv) as one row per peptide per sample, with the sample's intensity and detection type as columns.	pymzlib.readers.read_quantified_peptides	mzlib::readers::read_quantified_peptides_with	readers_read_quantified_peptides	readers read-quantified-peptides
Read any file mzLib recognises into a table of that format's own record fields, naming every field that could not become a column.	pymzlib.readers.read_records	mzlib::readers::read_records_with	readers_read_records	readers read-records
Read a result file through the cross-format quantifiable view: sequence, retention time, charge, theoretical mass, decoy flag and protein groups, the same columns for every format that offers it.	pymzlib.readers.read_results	mzlib::readers::read_results_with	readers_read_results	readers read-results
Read the scans of a spectra file: every scan's header always, and its peak arrays only on request.	pymzlib.readers.read_spectra	mzlib::readers::read_spectra_with	readers_read_spectra	readers read-spectra

sdrf · guide

You want to	Python	Rust	R	Wire verb
Decide whether each SDRF file's sample half describes an experimental design - Informative, Partial or Skeleton - with the per-column counts behind the verdict.	pymzlib.sdrf.assess	mzlib::sdrf::assess	sdrf_assess	sdrf assess
Read a label-free experimental design out of an SDRF, in MetaMorpheus's terms, or every reason it was refused.	pymzlib.sdrf.design	mzlib::sdrf::design_with	sdrf_design	sdrf design
Find the concepts a set of SDRF documents wrote inconsistently, one row per finding and spelling.	pymzlib.sdrf.lint	mzlib::sdrf::lint_labelled	sdrf_lint	sdrf lint
Read characteristics[age] cells into years with an honest precision, refusing any cell that would need a guess.	pymzlib.sdrf.parse_ages	mzlib::sdrf::parse_ages	sdrf_parse_ages	sdrf parse-age
Merge several SDRF documents into one analysis table, stamping each row with the document it came from.	pymzlib.sdrf.pool	mzlib::sdrf::pool_with	sdrf_pool	sdrf pool
Read one SDRF-Proteomics file as its header and rows of raw cells, keeping repeated column names and ragged rows exactly as written.	pymzlib.sdrf.read	mzlib::sdrf::read_with	sdrf_read	sdrf read
One row per sample, column and position: what each source name's rows agree on, the columns they disagree about named and withheld, and characteristics[age] read into years.	pymzlib.sdrf.samples	mzlib::sdrf::samples	sdrf_samples	sdrf samples
Check SDRF-Proteomics files against the specification's structural rules, one row per finding.	pymzlib.sdrf.validate	mzlib::sdrf::validate	sdrf_validate	sdrf validate

stats · guide

You want to	Python	Rust	R	Wire verb
Adjust a list of p-values for the false discovery rate with Benjamini-Hochberg, keeping every input position and leaving untested entries out of the family.	pymzlib.stats.adjust	mzlib::stats::adjust	stats_adjust	stats adjust
Fit one linear model per feature of a feature-by-sample table and test each named coefficient with limma's empirical-Bayes moderated t, Benjamini-Hochberg adjusted, in one call.	pymzlib.stats.fit	mzlib::stats::fit_with	stats_fit	stats fit
Pool one effect size per study into a random-effects estimate per feature (DerSimonian-Laird), with heterogeneity, direction agreement and the largest leave-one-out change.	pymzlib.stats.meta	mzlib::stats::meta_with	stats_meta	stats meta

version

You want to	Python	Rust	R	Wire verb
Report the bridge's version, its wire protocol, its .NET runtime, the mzLib it was built from, and every verb it dispatches.	pymzlib.bridge_version	mzlib::bridge_version	mzlibr_bridge_version	version