Table 1.
Overview of platforms for the analysis of big MS data of acquired mass spectra from MALDI–TOF MS. MDS: Multi-dimensional Scaling; PCA: principal component analysis; QA/QC: Quality Assurance/Quality Control; SOM: self-organization Map.
| Platform | Statistical Analysis | Spectra Analysis | Accepted Formats | URL | Reference |
|---|---|---|---|---|---|
| BioNumerics | ANOVA, MANOVA, PCA, MDS, SOM and other statistical, parametric and non-parametric tests. Dendograms, cluster analysis, bioclustering, generation of phylogenetic trees. QA/QC. |
Creation, identification and classification (spectrum libraries). Pre-processing: optimization, normalization, alignment, subtraction, smoothing. Peak detection, identification and quantification. |
mzML, *.btmsp, *.txt RAW |
https://www.applied-maths.com/applications/maldi-tof-bacterial-identification (accessed on 19 July 2021) | Bionumerics™ software (Applied Maths BVBA, Sint-Martens-Lantem, Belgium). |
| MaldiQUANT | Computational framework in R language: statistical analysis, dendograms, clustering, probability distributions, quality control, etc. | Pre-processing: optimization, normalization, alignment, subtraction, smoothing. Peak detection, identification, and quantification. | mzML, mzXLM, imzML *.csv, *.fid, *.tab | http://strimmerlab.org/software/maldiquant/ (accessed on 19 July 2021) | Gibb S and Strimmer [82] |
| Mass-Up | PCA, classification analysis, biomarker discovery, clustering and bioclustering. QA/QC. |
Preprocessing: intensity transformation, optimization, alignment, subtraction, smoothing and peak analysis. Peak detection and identification. | mzML, mzXLM, *.csv, *.muc | http://www.sing-group.org/mass-up/ (accessed on 19 July 2021) | López-Fernandez et al. [83] |
| MATLAB | Regression, ANOVA, PCA, multivariate analysis, probability distributions, cluster analysis. |
Pre-processing: optimization, smoothing, alignment, signal statistics, peak analysis, envelope extraction. Spectral analysis. |
*.txt, *.xls, *.xlsx |
http://es.mathworks.com/products/matlab-online/ (accessed on 19 July 2021) | MATLAB® software (MathWorks Inc., Natick, MA, USA) |
| PEAKS | Algorithms and support for analysis. | Pre-processing: optimization, normalization, alignment, subtraction, smoothing, peak analysis. Peak detection, identification and quantification. Sequence editor. |
mzML, mzXLM, mzDATA, MGF, ASCII | http://www.bioinfor.com/ (accessed on 19 July 2021) | Peaks® software (Bioinformatics Solutions Inc., Waterloo, ON, Canada) |