Concepts

Four ideas to keep in your head while you use mscompress:

• mzML — the input format, an uncompressed XML wrapper around base64-encoded binary arrays.
• MSZ — the compressed format mscompress produces. Three streams (XML, m/z, intensity) compressed independently so individual spectra are randomly addressable.
• MSZX — a tar archive bundling an MSZ file with annotation files (pepXML, Percolator TSV) and a JSON manifest.
• Lossy vs lossless — which compression path you take depends on whether you can tolerate precision loss on m/z and intensity arrays.