AStream

MAIN

AStream is an R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data. AStream detects isotopic, fragment and adduct patterns by identifying feature pairs that fulfill expected relational patterns. Data reduction by AStream allows compounds to be identified reliably and subsequently linked to metabolite databases. AStream provides researchers with a fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing consistency of results.

Alonso A, Julià A, Beltran A, Vinaixa M, Díaz M, Ibañez L, Correig X, Marsal S. AStream: an R package for annotating LC/MS metabolomic data. Bioinformatics . 2011 May 1;27(9):1339-40. Epub 2011 Mar 16. PMID: 21414990

VERSION 2.0

AStream has been recently updated to version 2.0. User suggestions have been taken into account in order to offer new functionalities as well as to solve compatibility issues between the different R versions. The main new functionalities included in this new version are listed below and can also be explored by using the R example on "help(AStream)":

Output features:

Users can export their results into a web report (i.e. see example here) which greatly facilitates interpretation.
Identification is performed on the HMDB metabolites using their monoisotopic mass and their biofluid/tissue location.

Optimized correlation matrix computation:

The matrix object size where the correlation results are stored is dynamically expanded by blocks if required.
Added option to perform extra feature pair filtering before correlation computation. This pre-filtering step is based on the expected m/z differences for the isotopic and/or adduct patterns. Filtering by m/z differences in addition to retention time differences speeds up computation time since correlation is calculated on a reduced set of feature pairs.

Isotopic patterns:

An upper intensity ratio threshold has been included. Feature pairs which intensity ratio exceeds this threshold are not further considered as an isotopic pattern.
The linear regression model linking m/z values and intensity ratios of isotopic patterns is iteratively computed until any residual exceeds X times the residual standard deviation.

DOWNLOADS

Version 2.0 (2014, R version >= 3.0.1)	Version 1.0 (2011)
Package Source: AStream_2.0.tar.gz	Package Source: AStream_1.0.tar.gz
Windows Binary: AStream_2.0.zip	Windows Binary: AStream_1.0.zip
New tutorial: R> help(AStream)	Old tutorial: Link
The AStream package depends on the "multtest", "Biobase" and “plotrix" packages. The following R commands install them from the CRAN and Bioconductor package repositories: > source("http://www.bioconductor.org/biocLite.R") > biocLite("Biobase") > biocLite("plotrix") > biocLite("multtest")