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aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Authors :
Rosenberger, George
Ludwig, Christina
Röst, Hannes L.
Aebersold, Ruedi
Malmström, Lars
Source :
Bioinformatics. Sep2014, Vol. 30 Issue 17, p2511-2513. 3p.
Publication Year :
2014

Abstract

Motivation: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking.Results: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.Availability and implementation: aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).Contact: lars.malmstroem@imsb.biol.ethz.chSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
13674803
Volume :
30
Issue :
17
Database :
Academic Search Index
Journal :
Bioinformatics
Publication Type :
Academic Journal
Accession number :
97825445
Full Text :
https://doi.org/10.1093/bioinformatics/btu200