Finnee - A Matlab toolbox for separation techniques hyphenated high resolution mass spectrometry dataset

Abstract

Post processing of dataset obtained using separation techniques hyphenated with mass spectrometry can allow automation of the recovery of target information, improve the visualization of the data or allow for mathematical separations of convoluted data. Despite the growing popularity and proven successes, those techniques are still only used by few. This is mainly due to the supposed difficulty to open hyphenated dataset, as well as use or develop efficient chemometrics tools. However, due to the work of the Human Proteome Organization (HUPO), the IUPAC and others, there is now MS file formats that are vendor-neutral and can easily be open using various language such as Java, Python, Matlab or R. In the past decades, using those formats, various tools (commercially or freely available) have been designed to help in the post-processing of hyphenated datasets. For proteomic applications, the best known is probably XCMS. However, each of these software is designed for a particular purpose and will not fit all purposes. In the context of our work, we developed a Matlab toolbox that allows openning of MS files in the mzML format and perform various calculations. The aim of this manuscript is to present this toolbox, called Finnee, as well as some key functions. While it is necessary to own a working Matlab license, the toolbox can be used without any programing skills. Every function is protected with the BSD license allowing anyone to study the source code, modify and share it, as long as its copyright notices and the license's disclaimers of warranty are maintained. The source code is available and will be maintain in the GitHub repository (https://github.com/glerny/finnee). Updates and tutorials will be posted in https://finneeblog.wordpress.com/.