Finnee2016 is a Matlab toolbox that was specifically designed to analyse analytical separation techniques hyphenated with high-resolution mass spectrometry (X-HRMS). Finnee2016 is not a software, it is a collection of classes and functions that allow recovering MS scans from mzML files and performed transformation (baseline drift correction, peak picking, centroid algorithms…), As a toolbox Finnee2016 cannot be used without a Matlab working. Finnee2016 has been designed with Matlab2016a, but most of the functions also work with older versions. While a basic knowledge of Matlab is needed, Finnee2016 has been designed as to allow to use it without programming skills. Operations are run by entering the correct line in Matlab command panel.
# Finnee2016, what is the point?
Every commercial instrument comes with software that allows analysing acquired X-HRMS data, so what the point of developing or learning a new software? Well, commercial software is often design for mass spectrometer used as standalone instruments and does not fully take advantage of the separation side. Chemometrics and bioinformatics apply to X-HRMS information are very dynamic fields especially in proteomics and metabolomics. Excellent software such as [xcms](https://xcmsonline.scripps.edu) and [mzMine2](http://mzmine.github.io/) have already been developed. The aim of FInnee2016 is not to copy them using another language. Finnee2016 is specifically designed for high-resolution mass spectrometry with MS^1 experiment but is not specific for a particular field. Moreover, Finnee2016 ambitions to provide a comprehensive analysis from a single dataset. The key approach is to extract relevant and accurate data that perfectly described the results of the analysis.
Finnee2016 is not a finished product. It is in constant development and files are likely to be modified. Finnee2016 also aims to be a collaborative work; you can correct, comment or contact me if you would like some special features. You can also contact me or follow this project via [Research Gate](https://www.researchgate.net/project/Finnee-A-Matlab-toolbox-for-post-processing-of-separation-techniques-hyphenated-high-resolution-mass-spectrometry).
Guillaume Erny (2021). glerny/Finnee2016 (https://github.com/glerny/Finnee2016), GitHub. Retrieved .
Extremely versatile and useful tool for anyone in the proteomics/metabolomics field. The toolbox allows one to extract a plethora of useful information that aide in the scientific investigation that include peak lists, cluster plots and centergrams all the while allowing one full precise control over parameters used in baseline correction and noise reduction from mzML files. I would highly recommend anyone to try it out as it has assisted me greatly in my scientific escapades.
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