CAMERA

Description

This module uses Bioconductor's CAMERA (Collection of Algorithms for MEtabolite pRofile Annotation) [1]. The algorithm involves three steps:

  1. Peaks are grouped according to their retention times.
  2. Within each group, clusters of isotope peaks are identified.
  3. Groups of peaks are sub-divided into smaller groups of peaks whose shapes are highly correlated. Clusters of isotopes are preserved, i.e. not separated into different groups.

The groups of peaks produced at the end of this process are referred to as pseudo-spectra; one per group. An identity is added to each peak indicating which pseudo-spectrum it is a member of. The identity also notes any peaks that were identified as isotopes.

Peak list showing pseudo-spectra identities.

Method parameters

FWHM Sigma
A Gaussian is fitted to each peak. This parameter multiplies the width of the fitted peak when grouping by peaks by their retention times.
FWHM percentage
The percentage of a peak's full-width half-maximum used when grouping peaks by their retention times.
Isotopes max. charge
The maximum charge considered when identifying isotopes.
Isotopes max. per cluster
The maximum number of isotopes per cluster.
Isotopes mass tolerance
The mass tolerance used when identifying isotopes. Provide both the absolute (m/z) and relative (ppm) values.
Correlation threshold
The minimum correlation required between two peaks' chromatograms when grouping by peak shape.
Correlation p-value
The required p-value when testing the significance of peak shape correlation.

Requirements

This module relies on Bioconductor's CAMERA package for R [2]. Therefore, you must have R v2.15 or later installed. To install the CAMERA package, run R and issue the following commands:

source("http://bioconductor.org/biocLite.R")
biocLite("CAMERA")

To run R from MZmine the Rserve package [3] must be installed in R, so also run the following R command:

install.packages("Rserve")

References

[1] Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Annotation of LC/ESI-MS Mass Signals" Proc. of BIRD 2007: First International Conference on Bioinformatics Research and Development, 2007. http://www.springerlink.com/content/473l404001787974/

[2] Bioconductor CAMERA "Collection of annotation related methods for mass spectrometry data" http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html.

[3] Rserve "A TCP/IP server which allows other programs to use facilities of R" https://rforge.net/Rserve/.