What the inspector checks
The bounded single-pass scanner accepts plain mzML and indexedmzML wrappers, rejects DTD and entity declarations, checks XML tag structure, namespace and version evidence, unique IDs, list counts, run-to-instrument and precursor references, spectrum/chromatogram indexes, MS levels, retention-time units and ordering, observed m/z ranges, binary-array type/precision/compression declarations, encoded lengths, and decoded value counts where supported.
TIC, BPC, and acquisition metadata
Total ion current and base-peak traces come from explicit uncompressed chromatogram time/intensity pairs when the arrays can be decoded. Otherwise the chart uses scan start time plus per-spectrum total-ion-current or base-peak-intensity CV terms. Run duration is the span between the earliest and latest usable scan times—not the wall-clock time spent acquiring or processing the file.
Binary-array boundary
The inspector inventories m/z, intensity, and time arrays; 32/64-bit numeric declarations; no-compression, zlib, and common MS-Numpress terms. Only uncompressed arrays are decoded. It does not silently treat unsupported compression as raw values, and it never fetches external schemas, vocabularies, or source data.
Acquisition-QC boundary
This is a structural metadata preflight, not a complete mzML validator or scientific quality decision. It does not validate every XSD or PSI-MS controlled-vocabulary rule, decode every compression combination, centroid/profile peaks, identify compounds, judge calibration or instrument performance, repair files, or certify suitability for research, clinical, or regulatory work. Confirm findings with trusted proteomics software and domain review.
Frequently asked questions
Why is a chromatogram listed but not graphed?
Its time/intensity arrays may be compressed, use unsupported numeric metadata, omit required type terms, or have inconsistent lengths. The array inventory preserves that evidence without inventing decoded points.
Why is run duration unavailable?
Duration requires usable scan start times with recognized seconds, minutes, or milliseconds units. A file may be structurally readable while omitting that metadata.
Does a clean result prove the experiment was good?
No. A clean result means only that the supported structural and metadata checks found no errors. It says nothing about sample preparation, calibration, sensitivity, identification, quantitation, or biological interpretation.
Authoritative references
The HUPO Proteomics Standards Initiative maintains the mzML specification, schemas, and examples. Element and attribute structure follows the official mzML 1.1 XML Schema; accessions and meanings are identified against the PSI-MS controlled vocabulary.
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