preprocessMS

Spectra. A MALDIquant object. An output of either <code><a rd-options="MALDIquantForeign" href="/link/importMzXml?package=MGMS2&version=1.0.2&to=MALDIquantForeign" data-mini-rdoc="MALDIquantForeign::importMzXml">importMzXml</a></code> or <code><a rd-options="" href="/link/filtermass?package=MGMS2&version=1.0.2" data-mini-rdoc="MGMS2::filtermass">filtermass</a></code>.

spectra

halfWindowSize The highest peaks in the given window (+/-halfWindowSize) will be recognized as peaks. (Default: 20). See <code><a rd-options="MALDIquant" href="/link/detectPeaks?package=MGMS2&version=1.0.2&to=MALDIquant" data-mini-rdoc="MALDIquant::detectPeaks">detectPeaks</a></code> for details.

halfWindowSize

SNIP.iteration An iteration used to remove the baseline of an spectrum. (Default: 60). See <code><a rd-options="MALDIquant" href="/link/removeBaseline?package=MGMS2&version=1.0.2&to=MALDIquant" data-mini-rdoc="MALDIquant::removeBaseline">removeBaseline</a></code> for details.

SNIP.iteration

Internal function. This function preprocesses spectra by transforming/smoothing intensity, removing baseline, and calibrating intensities.

A glycolipid mass spectrometry technology has the potential to accurately identify individual bacterial species from polymicrobial samples. To develop bacterial identification algorithms (e.g. machine learning) using this glycolipid technology, it is necessary to generate a large number of various in-silico polymicrobial mass spectra that are similar to real mass spectra. 'MGMS2' (Membrane Glycolipid Mass Spectrum Simulator) generates such in-silico mass spectra, considering errors in m/z (mass-to-charge ratio) and variances of intensity values, occasions of missing signature ions, and noise peaks. It estimates summary statistics of monomicrobial mass spectra for each strain or species and simulates polymicrobial glycolipid mass spectra using the summary statistics of monomicrobial mass spectra. References: Ryu, S.Y., Wendt, G.A., Chandler, C.E., Ernst, R.K. and Goodlett, D.R. (2019) <doi:10.1021/acs.analchem.9b03340> "Model-based Spectral Library Approach for Bacterial Identification via Membrane Glycolipids." Gibb, S. and Strimmer, K. (2012) <doi:10.1093/bioinformatics/bts447> "MALDIquant: a versatile R package for the analysis of mass spectrometry data."

George Wendt

MGMS2

'MGMS2' for Polymicrobial Samples

So Young Ryu

preprocessMS function

Spectra. A MALDIquant object. An output of either <code><a rd-options='MALDIquantForeign' href='importMzXml'>importMzXml</a></code> or <code><a rd-options='' href='filtermass'>filtermass</a></code>.

halfWindowSize The highest peaks in the given window (+/-halfWindowSize) will be recognized as peaks. (Default: 20). See <code><a rd-options='MALDIquant' href='detectPeaks'>detectPeaks</a></code> for details.

SNIP.iteration An iteration used to remove the baseline of an spectrum. (Default: 60). See <code><a rd-options='MALDIquant' href='removeBaseline'>removeBaseline</a></code> for details.

preprocessMS: preprocessMS

Description

Usage

Arguments

Value