filtermass

Mass Spectra (A MALDIquant MassSpectrum (S4) object). An output of <code><a rd-options="MALDIquantForeign" href="/link/importMzXml?package=MGMS2&version=1.0.2&to=MALDIquantForeign" data-mini-rdoc="MALDIquantForeign::importMzXml">importMzXml</a></code>.

spectra

Mass (m/z) range (a vector). For exmaple, c(1000,2200).

mass.range

Internal function. This function removes peaks with their mass values (m/z values) outside a given mass range.
This function is used in <code><a rd-options="" href="/link/process_monospectra?package=MGMS2&version=1.0.2" data-mini-rdoc="MGMS2::process_monospectra">process_monospectra</a></code>.

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

filtermass function

Mass Spectra (A MALDIquant MassSpectrum (S4) object). An output of <code><a rd-options='MALDIquantForeign' href='importMzXml'>importMzXml</a></code>.

Internal function. This function removes peaks with their mass values (m/z values) outside a given mass range.
This function is used in <code><a rd-options='' href='process_monospectra'>process_monospectra</a></code>.

filtermass: filtermass

Description

Usage

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Value