identifyComp: Identification of compounds

In erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Identification of compounds

Description

Identification of compounds. Each empirical spectrum is compared against a ms library.

Usage

identifyComp(Experiment, id.database = mslib,mz.range = NULL, n.putative = 3)

## S4 method for signature 'MetaboSet'
identifyComp(Experiment, id.database = mslib, mz.range = NULL, n.putative = 3)

Arguments

Experiment	A 'MetaboSet' S4 object containing the experiment data previously created by newExp, deconvolved by deconvolveComp and optionally aligned by alignComp.
id.database	The mass-spectra library to be compared with the empirical spectra. By default, the MassBank-[2] - Mass Bank of North America (MoNa) database are employed.
mz.range	The same as in alignComp. If specified already in alignComp, then there is no need to especify it again. If not, it has to be specified.
n.putative	The number of hits (compound candidate names) to be returned for each spectrum found.

Value

The function returns an updated S4 'MetaboSet' class, where the GC-MS samples have been now aligned.

Author(s)

Xavier Domingo-Almenara. [e-mail]

References

[1] Xavier Domingo-Almenara, et al., eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC-MS-Based Metabolomics. Analytical Chemistry (2016). DOI: 10.1021/acs.analchem.6b02927

[2] MassBank: A public repository for sharing mass spectral data for life sciences, H. Horai, M. Arita, S. Kanaya, Y. Nihei, T. Ikeda, K. Suwa. Y. Ojima, K. Tanaka, S. Tanaka, K. Aoshima, Y. Oda, Y. Kakazu, M. Kusano, T. Tohge, F. Matsuda, Y. Sawada, M. Yokota Hirai, H. Nakanishi, K. Ikeda, N. Akimoto, T. Maoka, H. Takahashi, T. Ara, N. Sakurai, H. Suzuki, D. Shibata, S. Neumann, T. Iida, K. Tanaka, K. Funatsu, F. Matsuura, T. Soga, R. Taguchi, K. Saito and T. Nishioka, J. Mass Spectrom., 45 (2010) 703-714.

See Also

newExp alignComp setAlPar setDecPar

erah documentation built on June 22, 2024, 11:01 a.m.