Quickstart: vendor2mzml

vendor2mzml auto-detects the vendor format of its input and writes mzML (or a gzipped mzML, or a metadata summary).

Convert

# Thermo .raw
vendor2mzml convert sample.raw sample.mzML

# Bruker .d bundle directory
vendor2mzml convert sample.d sample.mzML --indexed

# Waters .raw bundle directory, gzipped output
vendor2mzml convert sample.raw sample.mzML.gz

--indexed writes the standards-compliant <indexList> plus SHA-1 hash, so downstream tools (mzML2HDF, ProteoWizard's msconvert, MzIdentML builders) can index-jump into the file.

Validate

vendor2mzml validate sample.raw
vendor2mzml validate sample.mzML
vendor2mzml validate --json sample.d

validate accepts any input convert accepts (Thermo .raw, Bruker .d, Waters .raw) plus pre-existing mzML files (.mzML, .mzML.gz, read via mzdata). It runs the conformance harness from openproteo-core:

• monotonic spectrum indices,
• non-negative, non-decreasing retention times,
• equal-length m/z and intensity arrays,
• equal-length mobility arrays (if present),
• MS-level / polarity sanity,
• precursor presence on MSn spectra.

--json emits a single JSON object suitable for jq:

{"ok":true,"input":"sample.mzML","kind":"mzML","spectrum_count":3047,"elapsed_sec":0.214}

On failure, ok is false and error_kind names the conformance variant (for example, PeakArrayLengthMismatch).

Profile a run

vendor2mzml convert sample.raw sample.mzML --profile json

emits one JSON object on stderr after the conversion completes:

{"output":"sample.mzML","indexed":false,"spectra":3047,"elapsed_sec":0.812}

Use --profile text for a human-readable variant.

Inspect without converting

vendor2mzml info sample.d

vendor:        bruker
path:          sample.d
instrument:    timsTOF Pro (MS:1003005)
source format: Bruker TDF format (MS:1002817)
native id:     Bruker TDF nativeID format (MS:1002818)
software:      opentimstdf 1.0.4
spectra:       24425
  ms1:         1132
  ms2:         23293
  pos:         24425
rt range:      240.291 - 900.132 s (4.00 - 15.00 min)
decode time:   2.05 s

--json switches the output to a single JSON object suitable for piping into jq.

Exit codes

Code	Meaning
0	Success.
1	I/O error, or convert failed (unsupported format / vendor).
2	validate: input format was not recognised (clap errors also).
3	validate: the conformance harness rejected the input.