mzParquet Converter

Convert mass spectrometry vendor files to the open .mzparquet (opens in a new tab) format.

Download from the mzParquet Converter releases page (opens in a new tab).

GUI Application

The mzParquet Converter GUI provides a desktop application for converting vendor raw files to .mzparquet without using the command line.

Note: Thermo .raw conversion is not available on macOS due to ThermoFisher library limitations.

Features:

• Drag and drop — drop .raw files or .d folders directly onto the window
• Browse — click to select files via a file dialog
• Batch conversion — queue multiple files and convert them all at once
• Progress tracking — real-time progress percentage for each file
• Skip existing — automatically detects already-converted files (with option to force re-convert)

CLI Downloads

ThermoParquet — Thermo .raw → .mzparquet

Note: ThermoParquet requires the ThermoFisher RawFileReader runtime, which is only available on Windows and Linux.

dotD2parquet — Bruker .d → .mzparquet

Supported Instruments

Usage

# Thermo .raw → .mzparquet
ThermoParquet sample.raw
# Output: sample.mzparquet
 
# Bruker .d → .mzparquet
dotD2parquet sample.d
# Output: sample.mzparquet

Batch conversion (shell)

# Convert all .raw files in a directory
for f in *.raw; do ThermoParquet "$f"; done
 
# Convert all .d folders
for d in *.d; do dotD2parquet "$d"; done

Batch conversion (PowerShell)

# Convert all .raw files
Get-ChildItem *.raw | ForEach-Object { .\ThermoParquet.exe $_.FullName }
 
# Convert all .d folders
Get-ChildItem -Directory *.d | ForEach-Object { .\dotD2parquet.exe $_.FullName }

Output Format

The .mzparquet file is an Apache Parquet file with Zstandard compression and the following schema:

Files can be read with any Parquet library — Python (pyarrow, polars, pandas), R (arrow), Rust, etc.

import polars as pl
 
df = pl.read_parquet("sample.mzparquet")
print(df.head())

Linux Compatibility

CLI binaries are built on Ubuntu 22.04 (glibc 2.35). Compatible distros:

Requires glibc ≥ 2.35. Check your version: ldd --version

ThermoParquet additionally requires libicu and openssl (pre-installed on most Ubuntu/Debian systems).