mspack is a C++ program for lossless and lossy mass spectrometry data compression, achieving a high compression ratio without sacrificing performance. It includes an example implementation for mzXML and mzML as well as a format-agnostic API.
- C++11 compatible compiler, preferably gcc/clang.
- While a Unix environment is not required, compiling on Windows using other compilers might fail due to missing headers.
- gzip, should already be installed on a Unix system. On Linux, please make sure to use the latest gzip version (gzip 1.10). The gzip included in macOS works as well.
- bsc for better, but slower compression (recommended)
The API is defined in include/mspack.h. The mspack binary represents an example implementation to showcase the capabilities of the program. Users are encouraged to use the API for advanced usage and to use the mspack transforms in other software.
Compile by running make in src/ directory. This will place the binary in the top directory. Running the program without arguments will provide a help interface explaining the program usage, including lossy and advanced options. Use the .mgz file extension to use the gzip backend and .bsc to use bsc, which will improve compression significantly, but slow down compression.
mzML encode:
mspack --mzmle (options) <in> <out><.mgz|.bsc>
mzml decode:
mspack --mzmld <in><.mgz|.bsc> <out>
mzXML encode:
mspack --mzxmle (options) <in> <out><.mgz|.bsc>
mzXML decode:
mspack --mzxmld <in><.mgz|.bsc> <out>
The examples directory contains a test file which can be compressed using the following commands:
./mspack --mzmle examples/BSA1.mzml BSA.mgz
./mspack --mzmle examples/BSA1.mzml BSA.bsc
./mspack --mzmle --mz-fixed-abs --int-log examples/BSA1.mzml BSA-lossy.mgz
./mspack --mzmld BSA.bsc BSA-decoded.mzml
Due to the XML library we use, whitespace is not preserved in the decoded file, although this does not cause a functional difference for the decoded file as XML is invariant to the addition or removal of whitespace. SHA1 checksum tags are recalculated when needed.
The current implementation depends on the mz values being increasing. This is sometimes not the case if a third data point is present, i.e. ion mobility in addition to mz and intensity.
The implementation can only use raw mz and intensity arrays. If the arrays are compressed with e.g. zlib or msnumpress, the file can be converted using msconvert so it can be used by mspack.
The mzXML implementation does not support all features as the format has been superseded by mzML. mzXML is limited to 32-bit files and does not support the block-based I/O feature.
mspack is available under the Apache License. It uses the tinyxml2 library by Lee Thomason, SHA1 by Dominik Reichl and base64 by William Sherif. Consult the source code for license information of these libraries. The mspack XML parsing code is partially based on the parsing code of Masscomp by Ruochen Yang, Xi Chen, and Idoia Ochoa.
Felix Hanau and Idoia Ochoa, University of Illinois at Urbana-Champaign
