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

López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M - BMC Bioinformatics (2015)

Bottom Line: 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.Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers.

View Article: PubMed Central - PubMed

Affiliation: Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. hlfernandez@uvigo.es.

ABSTRACT

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 http://sing.ei.uvigo.es/mass-up.

No MeSH data available.


Related in: MedlinePlus

Classification analysis view. Classification analysis view presenting the result of executing a Bayes Net classifier using a 10-fold cross validation scheme. The resulting confusion matrix is presented along with several statistical measurements. ROC curve corresponding to condition C of the Wine dataset is also showed
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Fig5: Classification analysis view. Classification analysis view presenting the result of executing a Bayes Net classifier using a 10-fold cross validation scheme. The resulting confusion matrix is presented along with several statistical measurements. ROC curve corresponding to condition C of the Wine dataset is also showed

Mentions: Classification analyses are performed in the classification view (shown in Fig. 5), which was adapted from the Weka software. Through this view, the user can select a classifier and a validation scheme (i.e. cross-validation or percentage split) to perform an evaluation. As shown, the results report includes several global and per-class statistics, as well as the resulting confusion matrix. Using these operations, users can assess whether the data being analyzed is suitable for classification, as well as determine which classification algorithm is best.Fig. 5


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

López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M - BMC Bioinformatics (2015)

Classification analysis view. Classification analysis view presenting the result of executing a Bayes Net classifier using a 10-fold cross validation scheme. The resulting confusion matrix is presented along with several statistical measurements. ROC curve corresponding to condition C of the Wine dataset is also showed
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4595311&req=5

Fig5: Classification analysis view. Classification analysis view presenting the result of executing a Bayes Net classifier using a 10-fold cross validation scheme. The resulting confusion matrix is presented along with several statistical measurements. ROC curve corresponding to condition C of the Wine dataset is also showed
Mentions: Classification analyses are performed in the classification view (shown in Fig. 5), which was adapted from the Weka software. Through this view, the user can select a classifier and a validation scheme (i.e. cross-validation or percentage split) to perform an evaluation. As shown, the results report includes several global and per-class statistics, as well as the resulting confusion matrix. Using these operations, users can assess whether the data being analyzed is suitable for classification, as well as determine which classification algorithm is best.Fig. 5

Bottom Line: 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.Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers.

View Article: PubMed Central - PubMed

Affiliation: Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. hlfernandez@uvigo.es.

ABSTRACT

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 http://sing.ei.uvigo.es/mass-up.

No MeSH data available.


Related in: MedlinePlus