Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity o...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0094692 |
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| author | David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer |
| author_facet | David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer |
| author_sort | David Lyon |
| collection | DOAJ |
| description | Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover. |
| format | Article |
| id | doaj-art-d459744263114b5fa5bd3ac83fce802e |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-d459744263114b5fa5bd3ac83fce802e2025-08-20T03:46:11ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9469210.1371/journal.pone.0094692Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.David LyonMaria Angeles CastillejoChristiana StaudingerWolfram WeckwerthStefanie WienkoopVolker EgelhoferProtein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover.https://doi.org/10.1371/journal.pone.0094692 |
| spellingShingle | David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. PLoS ONE |
| title | Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. |
| title_full | Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. |
| title_fullStr | Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. |
| title_full_unstemmed | Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. |
| title_short | Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data. |
| title_sort | automated protein turnover calculations from 15n partial metabolic labeling lc ms shotgun proteomics data |
| url | https://doi.org/10.1371/journal.pone.0094692 |
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