chenxiptz / masscomp

a lossless compressor for mass spectrometry data

MassComp

About MassComp

MassComp is a loseless compressor for mass spectrometry data. It compresses the mass-to-charge ratio and intensity pairs in mzXML files efficiently by calculating the hexadecimal difference of consecutive m/z values, and by searching for parts of the intensity values that match previous ones. The remaining parts of the mzXML (e.g., metadata associated to the experiments) is compressed with the general compression algorithm 7zip.

Getting Started

Download the full project.

Run MassComp

Linux system

To compile:

g++ -o masscomp masscomp.cpp tinyxml2.cpp

To compress:

./masscomp -c fileOri.mzXML fileMasscomp

To decompress

./masscomp -d fileMasscomp fileDecomp.mzXML

To compare

./masscomp -cmp fileOri.mzXML fileDecomp.mzXML

Windows system

Current implementation of the code can be run by visual studio on windows system (we will provide a Linux and Mac implementation shortly).

Here's an example of this. Folder 'MSV000080896' is downloaded from MassIVE with id MSV000080896 and contains two mzXML files.

Run the executbale file MassComp in the project. With the hint "please input the path of files to be compressing:", input the folder path "\MSV000080896\peak\Data_mzXML" to start compressing. The output folder need an external compression with 7zip.

With the hint "please input the path of files to be decompressing:", input the folder path "\output\MSV000080896\peak\Data_mzXML" to start decompressing. Before start the decompressing, the zip file needs an external decompression with 7zip.

Note: Running the application in Windows uses gzip and requires installation of Cygwin.

Datasets

Datasets of mass spectrometry data can be downloaded from MassIVE https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp

Authors

MassComp was created by Ruochen Yang and Idoia Ochoa at University of Illinois at Urbana-Champaign.

Contact

If you have any problem, please email me at [email protected]