The spectra generated by MALDI apparatus usually contain a high level of noisy signals, making data preprocessing a crucial task that must be carried out before subsequent analysis. In addition, several open-source libraries to handle these data formats have been developed in the last years, among which the following are noteworthy: mzMatch, jmzML, jmzReader, the IO Framework and different R packages. These spectra are usually stored using open xml-based formats such as mzXML, mzML and PeakML. Each single spectrum contains thousands of measurements entailing mass-to-charge ratio (m/z) signals and intensity (i.e. Raw data generated by MALDI is usually composed of large spectra sets. In this sense, computational tools play a key role in MALDI experiments, as they are able to preprocess raw data registered in different formats, compare them, and apply complex algorithms in order to finally extract new knowledge and useful conclusions. The aforementioned reasons have led to the use MALDI for the classification of large sets of samples from different sources and/or characteristics. Large sets of samples are analysed quickly in one single batch. Mass spectrometry using matrix assisted laser desorption ionization coupled to time of flight analysers, MALDI-TOF-MS, referred to herein as MALDI, has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. Mass-Up is distributed under license GPLv3 and it is open and free to all users at. Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up software allows data preprocessing, as well as subsequent analysis including ( i) biomarker discovery, ( ii) clustering, ( iii) biclustering, ( iv) three-dimensional PCA visualization and ( v) classification of large sets of spectra data. Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. Mass spectrometry is one of the most important techniques in the field of proteomics.
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