A critical comparison of three MS‐based approaches for quantitative proteomics analysis
Abstract MS‐based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data‐dependent metho...
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crwiley:10.1002/jms.4669 2024-09-15T18:03:49+00:00 A critical comparison of three MS‐based approaches for quantitative proteomics analysis Taverna, Domenico Gaspari, Marco 2020 http://dx.doi.org/10.1002/jms.4669 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jms.4669 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jms.4669 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Journal of Mass Spectrometry volume 56, issue 1 ISSN 1076-5174 1096-9888 journal-article 2020 crwiley https://doi.org/10.1002/jms.4669 2024-07-25T04:19:58Z Abstract MS‐based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data‐dependent methods for protein relative quantification (label‐free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole‐Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label‐based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold‐changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field. Article in Journal/Newspaper DML Wiley Online Library Journal of Mass Spectrometry 56 1 |
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English |
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Abstract MS‐based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data‐dependent methods for protein relative quantification (label‐free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole‐Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label‐based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold‐changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field. |
format |
Article in Journal/Newspaper |
author |
Taverna, Domenico Gaspari, Marco |
spellingShingle |
Taverna, Domenico Gaspari, Marco A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
author_facet |
Taverna, Domenico Gaspari, Marco |
author_sort |
Taverna, Domenico |
title |
A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
title_short |
A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
title_full |
A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
title_fullStr |
A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
title_full_unstemmed |
A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
title_sort |
critical comparison of three ms‐based approaches for quantitative proteomics analysis |
publisher |
Wiley |
publishDate |
2020 |
url |
http://dx.doi.org/10.1002/jms.4669 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jms.4669 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jms.4669 |
genre |
DML |
genre_facet |
DML |
op_source |
Journal of Mass Spectrometry volume 56, issue 1 ISSN 1076-5174 1096-9888 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/jms.4669 |
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Journal of Mass Spectrometry |
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56 |
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1 |
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1810441281679130624 |