Mass-Up: An all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery

H. López-Fernández, H. M. Santos, J. L. Capelo, Florentino Fdez-Riverola, D. Glez-Peña, Miguel Reboiro-Jato

Research output: Contribution to journalArticle

52 Citations (Scopus)


Background: Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. 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. Results: Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. 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. Conclusions: Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at

Original languageEnglish
Article number318
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 5 Oct 2015


  • Biomarker discovery
  • Knowledge discovery
  • Machine learning
  • Mass spectrometry

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