Glossary

A reference for terms used throughout this specification.

Apache Arrow

An in-memory columnar data model that shares Parquet's columnar abstraction; Arrow and Parquet schemas map to one another and are straightforward to convert between.

Apache Parquet

The strongly-typed, compressed, columnar on-disk format in which each facet of an mzPeak archive is stored. See Anatomy of a Parquet file.

Centroid

A spectrum (or peak list) reduced to discrete m/z–intensity peaks, as opposed to profile data.

Chromatogram

A measurement over time (for example a total ion current or extracted-ion trace); one of the mzPeak entity types. See Entity Type.

Chunked layout

A signal-data layout that cuts the sorted main axis into non-overlapping chunks (for example fixed m/z windows) — recording each chunk's start, end, and index — to allow random access along the axis. See Chunked Layout.

Controlled vocabulary (CV)

A curated set of defined terms with stable accessions, used to annotate metadata unambiguously. mzPeak uses the PSI-MS controlled vocabulary.

CURIE

A compact URI of the form prefix:reference (for example MS:1000559) used to reference a controlled-vocabulary term.

Data kind

An index-file field declaring a member's semantics and expected schema family: data arrays, peaks, metadata, proprietary, or other. See Data Kind.

Delta encoding

An opaque transform that stores successive differences instead of absolute values, compressing sorted axes such as m/z efficiently.

Entity type

An index-file field declaring what a member describes: spectrum, chromatogram, wavelength spectrum, or other. See Entity Type.

HUPO-PSI

The Human Proteome Organization Proteomics Standards Initiative, the body that governs mzPeak and maintains the PSI-MS controlled vocabulary.

imzML

The mzML-derived open standard for mass-spectrometry imaging data (XML plus an .ibd binary sidecar).

Index file (mzpeak_index.json)

The JSON manifest listing every archive member with its entity_type and data_kind, so a reader resolves files by meaning rather than by name. See Index File.

Ion mobility

A gas-phase separation dimension (for example drift time or 1/K0) that may be stored as an array parallel to m/z and intensity.

m/z

Mass-to-charge ratio; the primary measurement axis of a mass spectrum.

mzML

The HUPO-PSI XML standard for mass-spectrometry data; mzPeak draws on its data model and reuses concepts such as controlled vocabularies where feasible.

mzPeak

An open, columnar mass-spectrometry data format: a ZIP archive (or directory) of Apache Parquet facets plus a JSON index, annotated using the PSI-MS controlled vocabulary under HUPO-PSI.

Null marking

A profile-data compression technique that replaces flanking zero-intensity points with null m/z and intensity values — so Parquet stores only a validity bit — reconstructing positions from a fitted m/z-spacing model. See Null Marking.

Numpress (MS-Numpress)

A family of lossy and lossless numeric compression schemes for m/z and intensity arrays, usable in mzPeak as an opaque transform.

Opaque transform

A per-array encoding (for example delta encoding or Numpress) applied within a chunk and recorded so a reader can decode it. Some transforms (such as certain Numpress modes) are lossy.

Packed parallel metadata tables

The metadata layout that stores several related sub-tables (spectrum, scan, precursor, selected ion) side by side, linked by primary- and foreign-key index columns. See Packed Parallel Metadata Tables.

Page index

A Parquet footer structure — which mzPeak writers MUST emit — that enables random access below the row-group level.

Point layout

A signal-data layout that stores arrays as-is in parallel columns alongside a repeated entity-index column. See Point Layout.

Profile

A spectrum stored as a quasi-continuous trace of m/z–intensity samples, as opposed to centroid data.

PSI-MS CV

The controlled vocabulary of mass-spectrometry terms maintained by HUPO-PSI; the semantic backbone of mzPeak metadata.

Row group

A horizontal partition of a Parquet file — the unit of columnar compression and coarse random access.

Sorting rank

An array's ordering role within a signal layout; sorting rank 0 is the sorted "main axis" around which all parallel arrays are arranged. Arrays of differing length SHOULD instead be stored as auxiliary arrays.

Total ion current (TIC)

The summed intensity recorded for a spectrum; frequently traced over time as a chromatogram.

Zero-run stripping

A profile-data size reduction that removes all but the first and last zero-intensity points in empty regions of a spectrum. See Zero Run Stripping.