MALDIassist: Mathematical Utilities for MALDI-TOF Mass Spectrometry
Supports matrix-assisted laser desorption/ionization time-of-flight
(MALDI-TOF) mass spectrometry workflows from raw Bruker spectra to
cohort-level peak matrices. Provides spectrum loading, Savitzky-Golay
smoothing, baseline correction (SNIP and TopHat), Gaussian
kernel-regression-based peak detection including shoulder peaks,
peak-quality assessment, filtering, and cohort feature analysis.
Computationally intensive routines are implemented in C++ using 'Rcpp'.
The implemented signal-processing methods include those described by
Savitzky and Golay (1964) <doi:10.1021/ac60214a047>, Ryan et al. (1988)
<doi:10.1016/0168-583X(88)90063-8>, Stanford, Bagley and Solomon (2016)
<doi:10.1186/s12953-016-0107-8>, and Nadaraya-Watson kernel regression
(Nadaraya (1964) <doi:10.1137/1109020>; Watson (1964)
<https://www.jstor.org/stable/25049340>).
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