CLI Quick Start¶

After building, the binary is at ./cli/mscompress.

Compress¶

mscompress input.mzML output.msz

If the output path is omitted, the input filename with the .msz extension is used:

mscompress input.mzML        # → input.msz

Decompress¶

mscompress input.msz output.mzML

The input file's extension determines the direction — mscompress detects mzML vs MSZ from the file's magic bytes, not the extension.

Extract a subset¶

mscompress --extract-indices 0-100 input.msz subset.mzML
mscompress --extract-scans 1-3,5-6 input.msz subset.mzML
mscompress --ms-level 2 input.msz ms2-only.mzML

Inspect a file¶

mscompress --describe input.msz
mscompress --describe --json input.msz

List available algorithms¶

mscompress --list-algorithms
mscompress --list-algorithms --json

Lossy compression¶

mscompress --mz-lossy delta32 --int-lossy log input.mzML
mscompress --mz-lossy delta32 --mz-scale-factor 524288 input.mzML

See the profile picker and the algorithm catalog.