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