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Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments
BACKGROUND: Quality assessment methods, that are common place in engineering and industrial production, are not widely spread in large-scale proteomics experiments. But modern technologies such as Multi-Dimensional Liquid Chromatography coupled to Mass Spectrometry (LC-MS) produce large quantities o...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678124/ https://www.ncbi.nlm.nih.gov/pubmed/19351414 http://dx.doi.org/10.1186/1756-0381-2-4 |
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author | Schulz-Trieglaff, Ole Machtejevas, Egidijus Reinert, Knut Schlüter, Hartmut Thiemann, Joachim Unger, Klaus |
author_facet | Schulz-Trieglaff, Ole Machtejevas, Egidijus Reinert, Knut Schlüter, Hartmut Thiemann, Joachim Unger, Klaus |
author_sort | Schulz-Trieglaff, Ole |
collection | PubMed |
description | BACKGROUND: Quality assessment methods, that are common place in engineering and industrial production, are not widely spread in large-scale proteomics experiments. But modern technologies such as Multi-Dimensional Liquid Chromatography coupled to Mass Spectrometry (LC-MS) produce large quantities of proteomic data. These data are prone to measurement errors and reproducibility problems such that an automatic quality assessment and control become increasingly important. RESULTS: We propose a methodology to assess the quality and reproducibility of data generated in quantitative LC-MS experiments. We introduce quality descriptors that capture different aspects of the quality and reproducibility of LC-MS data sets. Our method is based on the Mahalanobis distance and a robust Principal Component Analysis. CONCLUSION: We evaluate our approach on several data sets of different complexities and show that we are able to precisely detect LC-MS runs of poor signal quality in large-scale studies. |
format | Text |
id | pubmed-2678124 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26781242009-05-07 Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments Schulz-Trieglaff, Ole Machtejevas, Egidijus Reinert, Knut Schlüter, Hartmut Thiemann, Joachim Unger, Klaus BioData Min Methodology BACKGROUND: Quality assessment methods, that are common place in engineering and industrial production, are not widely spread in large-scale proteomics experiments. But modern technologies such as Multi-Dimensional Liquid Chromatography coupled to Mass Spectrometry (LC-MS) produce large quantities of proteomic data. These data are prone to measurement errors and reproducibility problems such that an automatic quality assessment and control become increasingly important. RESULTS: We propose a methodology to assess the quality and reproducibility of data generated in quantitative LC-MS experiments. We introduce quality descriptors that capture different aspects of the quality and reproducibility of LC-MS data sets. Our method is based on the Mahalanobis distance and a robust Principal Component Analysis. CONCLUSION: We evaluate our approach on several data sets of different complexities and show that we are able to precisely detect LC-MS runs of poor signal quality in large-scale studies. BioMed Central 2009-04-07 /pmc/articles/PMC2678124/ /pubmed/19351414 http://dx.doi.org/10.1186/1756-0381-2-4 Text en Copyright © 2009 Schulz-Trieglaff et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Schulz-Trieglaff, Ole Machtejevas, Egidijus Reinert, Knut Schlüter, Hartmut Thiemann, Joachim Unger, Klaus Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title | Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title_full | Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title_fullStr | Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title_full_unstemmed | Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title_short | Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
title_sort | statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678124/ https://www.ncbi.nlm.nih.gov/pubmed/19351414 http://dx.doi.org/10.1186/1756-0381-2-4 |
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