| mzML |
HUPO-PSI XML format for mass spectrometry data. Input format for mscompress. |
| MSZ |
The compressed format mscompress produces. Three streams (XML, m/z, intensity), randomly addressable. |
| MSZX |
A tar archive bundling an MSZ file with annotation files and a JSON manifest. |
| Spectrum |
A single MS scan — m/z + intensity arrays plus metadata (scan number, MS level, retention time). |
| Scan |
A single mass-spectrometry measurement. "Scan number" is the original instrument-assigned identifier. |
| MS level |
1 for survey scans, 2 (or higher) for fragmentation scans. |
| m/z |
Mass-to-charge ratio, the x-axis of a spectrum. |
| Intensity |
Signal counts at a given m/z, the y-axis of a spectrum. |
| Peak |
An (m/z, intensity) pair within a spectrum. |
| Retention time |
Seconds since chromatographic separation began. |
| PSM |
Peptide-Spectrum Match — an identification result linking a peptide to a spectrum. |
| pepXML |
XML format for peptide identifications, output by many search engines. |
| Percolator |
A semi-supervised PSM rescoring tool. Its .pin files are tab-separated. |
| Croissant |
An ML metadata format describing datasets in a structured, joinable way. |
| Block |
A unit of ZSTD-compressed data within an MSZ stream. Block boundaries determine random-access granularity. |
| Division |
A worker thread's chunk of an MSZ file — a contiguous range of spectra. |
| Magic tag |
The 4-byte 0x035F51B5 identifier at the start of an MSZ file. |
| Algorithm |
A pre-compression transform on numeric arrays, registered in algo_registry. |
| Accession |
A PSI-MS ontology identifier. mscompress uses them to identify source data types (MS:1000521 = 32-bit float, etc.). |