A critical comparison of three MS‐based approaches for quantitative proteomics analysis
| العنوان: | A critical comparison of three MS‐based approaches for quantitative proteomics analysis |
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| المؤلفون: | Domenico Taverna, Marco Gaspari |
| المصدر: | Journal of Mass Spectrometry. 56 |
| بيانات النشر: | Wiley, 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | Proteomics, Analyte, Reproducibility, 010405 organic chemistry, Chemistry, Escherichia coli Proteins, 010401 analytical chemistry, Quantitative proteomics, Proteins, Reproducibility of Results, Diagnostic accuracy, Computational biology, Tandem mass tag, 01 natural sciences, Workflow, 0104 chemical sciences, Tandem Mass Spectrometry, Proteome, Soybean Proteins, False positive paradox, Humans, Spectroscopy, Chromatography, Liquid |
| الوصف: | 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. |
| تدمد: | 1096-9888 1076-5174 |
| DOI: | 10.1002/jms.4669 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c6c1ce6db44e30d11ced2ea67ae2e176 https://doi.org/10.1002/jms.4669 |
| Rights: | CLOSED |
| رقم الانضمام: | edsair.doi.dedup.....c6c1ce6db44e30d11ced2ea67ae2e176 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 10969888 10765174 |
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| DOI: | 10.1002/jms.4669 |