Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit

Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) .

SPUTNIK: an R package for peak selection of Mass spectrometry imaging data

If you find SPUTNIK useful, please consider citing our work :)

Inglese, P., Correia, G., Takats, Z., Nicholson, J. K. & Glen, R. C. (2018). SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data. Bioinformatics (Oxford, England)

Description

SPUTNIK is an R package consisting of a series of tools to filter mass spectrometry imaging peaks characterized by a noisy or unlikely spatial distribution. SPUTNIK can produce mass spectrometry imaging datasets characterized by a smaller but more informative set of peaks, reduce the complexity of subsequent multi-variate analysis and increase the interpretability of the statistical results.

Contact

• issues and bug reports: https://github.com/paoloinglese/SPUTNIK/issues
• pull requests: https://github.com/paoloinglese/SPUTNIK/pulls
• email contact: p.inglese at outlook.com

Install from CRAN

To install the CRAN package, run the command:

install.packages("SPUTNIK")

Install from source

To install it, run the command:

devtools::install_git("https://github.com/paoloinglese/SPUTNIK.git")

Example SPUTNIK workflow on MALDI mass spectrometry imaging data

https://paoloinglese.github.io/SPUTNIK/

Example data

Two mass spectrometry imaging datasets in RData format are available in a separate repository:

https://github.com/paoloinglese/SPUTNIKexamples