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Generic workflow for quality assessment of quantitative label-free LC-MS analysis

Sandin, Marianne LU ; Krogh, Morten LU ; Hansson, Karin M LU and Levander, Fredrik LU (2011) In Proteomics 11(6). p.1114-1124
Abstract
As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the... (More)
As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
quality control, LC-MS, label-free quantification
in
Proteomics
volume
11
issue
6
pages
1114 - 1124
publisher
John Wiley & Sons
external identifiers
  • wos:000288137700014
  • scopus:79952304665
ISSN
1615-9861
DOI
10.1002/pmic.201000493
language
English
LU publication?
yes
id
aca7b894-641a-498e-9862-e77919ed65bd (old id 1769470)
date added to LUP
2011-01-25 12:03:49
date last changed
2017-11-12 03:02:35
@article{aca7b894-641a-498e-9862-e77919ed65bd,
  abstract     = {As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed.},
  author       = {Sandin, Marianne and Krogh, Morten and Hansson, Karin M and Levander, Fredrik},
  issn         = {1615-9861},
  keyword      = {quality control,LC-MS,label-free quantification},
  language     = {eng},
  number       = {6},
  pages        = {1114--1124},
  publisher    = {John Wiley & Sons},
  series       = {Proteomics},
  title        = {Generic workflow for quality assessment of quantitative label-free LC-MS analysis},
  url          = {http://dx.doi.org/10.1002/pmic.201000493},
  volume       = {11},
  year         = {2011},
}