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Data processing methods and quality control strategies for label-free LC-MS protein quantification.

Sandin, Marianne LU ; Teleman, Johan LU ; Malmström, Johan LU and Levander, Fredrik LU (2014) In Biochimica et Biophysica Acta 1844(1). p.29-41
Abstract
Protein quantification using different LC-MS techniques is becoming a standard practice. However, with a multitude of experimental setups to choose from, as well as a wide array of software solutions for subsequent data processing, it is non-trivial to select the most appropriate workflow for a given biological question. In this review, we highlight different issues that need to be addressed by software for quantitative LC-MS experiments and describe different approaches that are available. With focus on label-free quantification, examples are discussed both for LC-MS/MS and LC-SRM data processing. We further elaborate on current quality control methodology for performing accurate protein quantification experiments. This article is part of... (More)
Protein quantification using different LC-MS techniques is becoming a standard practice. However, with a multitude of experimental setups to choose from, as well as a wide array of software solutions for subsequent data processing, it is non-trivial to select the most appropriate workflow for a given biological question. In this review, we highlight different issues that need to be addressed by software for quantitative LC-MS experiments and describe different approaches that are available. With focus on label-free quantification, examples are discussed both for LC-MS/MS and LC-SRM data processing. We further elaborate on current quality control methodology for performing accurate protein quantification experiments. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biochimica et Biophysica Acta
volume
1844
issue
1
pages
29 - 41
publisher
Elsevier
external identifiers
  • pmid:23567904
  • wos:000330911400005
  • scopus:84890571201
ISSN
0006-3002
DOI
10.1016/j.bbapap.2013.03.026
language
English
LU publication?
yes
id
aee3c50d-0f23-4103-b2a1-2f5ffc885a64 (old id 3734008)
date added to LUP
2013-05-22 14:53:45
date last changed
2017-11-05 03:55:34
@article{aee3c50d-0f23-4103-b2a1-2f5ffc885a64,
  abstract     = {Protein quantification using different LC-MS techniques is becoming a standard practice. However, with a multitude of experimental setups to choose from, as well as a wide array of software solutions for subsequent data processing, it is non-trivial to select the most appropriate workflow for a given biological question. In this review, we highlight different issues that need to be addressed by software for quantitative LC-MS experiments and describe different approaches that are available. With focus on label-free quantification, examples are discussed both for LC-MS/MS and LC-SRM data processing. We further elaborate on current quality control methodology for performing accurate protein quantification experiments. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era.},
  author       = {Sandin, Marianne and Teleman, Johan and Malmström, Johan and Levander, Fredrik},
  issn         = {0006-3002},
  language     = {eng},
  number       = {1},
  pages        = {29--41},
  publisher    = {Elsevier},
  series       = {Biochimica et Biophysica Acta},
  title        = {Data processing methods and quality control strategies for label-free LC-MS protein quantification.},
  url          = {http://dx.doi.org/10.1016/j.bbapap.2013.03.026},
  volume       = {1844},
  year         = {2014},
}