Multiple proteases to localize oxidation sites
Proteins present in cellular environments with high levels of reactive oxygen and nitrogen species and/or low levels of antioxidants are highly susceptible to oxidative post-translational modification (PTM). Irreversible oxidative PTMs can generate a complex distribution of modified protein molecule...
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| Veröffentlicht in: | PloS one 2015-03, Vol.10 (3), p.e0116606-e0116606 |
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| description | Proteins present in cellular environments with high levels of reactive oxygen and nitrogen species and/or low levels of antioxidants are highly susceptible to oxidative post-translational modification (PTM). Irreversible oxidative PTMs can generate a complex distribution of modified protein molecules, recently termed as proteoforms. Using ubiquitin as a model system, we mapped oxidative modification sites using trypsin, Lys-C, and Glu-C peptides. Several M+16 Da proteoforms were detected as well as proteoforms that include other previously unidentified oxidative modifications. This work highlights the use of multiple protease digestions to give insights to the complexity of oxidative modifications possible in bottom-up analyses. |
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Irreversible oxidative PTMs can generate a complex distribution of modified protein molecules, recently termed as proteoforms. Using ubiquitin as a model system, we mapped oxidative modification sites using trypsin, Lys-C, and Glu-C peptides. Several M+16 Da proteoforms were detected as well as proteoforms that include other previously unidentified oxidative modifications. This work highlights the use of multiple protease digestions to give insights to the complexity of oxidative modifications possible in bottom-up analyses.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0116606</identifier><identifier>PMID: 25775238</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino Acid Sequence ; Amino acids ; Analytical chemistry ; Animals ; Antioxidants ; Cattle ; Chromatography ; Complexity ; Fourier transforms ; Free radicals ; Identification ; Lipid peroxidation ; Mass spectrometry ; Methionine - metabolism ; Molecular Sequence Data ; Multiple database searches ; Nitrogen ; Oxidation ; Oxidation-Reduction ; Oxygen ; Peptide Hydrolases - chemistry ; Peptide Hydrolases - metabolism ; Peptides ; Post-translation ; Post-translational modifications ; Proteases ; Protein Processing, Post-Translational ; Proteins ; Proteolysis ; Proteomics ; Reactive nitrogen species ; Reactive oxygen species ; Scientific imaging ; Trypsin ; Ubiquitin ; Ubiquitin - metabolism</subject><ispartof>PloS one, 2015-03, Vol.10 (3), p.e0116606-e0116606</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Gu, Robinson. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Gu, Robinson 2015 Gu, Robinson</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-23b223cc4e89b4e2100db37404ac3e54ab08fe5099a8b781095488b725094e4d3</citedby><cites>FETCH-LOGICAL-c692t-23b223cc4e89b4e2100db37404ac3e54ab08fe5099a8b781095488b725094e4d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361631/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361631/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25775238$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ariga, Hiroyoshi</contributor><creatorcontrib>Gu, Liqing</creatorcontrib><creatorcontrib>Robinson, Renã A S</creatorcontrib><title>Multiple proteases to localize oxidation sites</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Proteins present in cellular environments with high levels of reactive oxygen and nitrogen species and/or low levels of antioxidants are highly susceptible to oxidative post-translational modification (PTM). Irreversible oxidative PTMs can generate a complex distribution of modified protein molecules, recently termed as proteoforms. Using ubiquitin as a model system, we mapped oxidative modification sites using trypsin, Lys-C, and Glu-C peptides. Several M+16 Da proteoforms were detected as well as proteoforms that include other previously unidentified oxidative modifications. This work highlights the use of multiple protease digestions to give insights to the complexity of oxidative modifications possible in bottom-up analyses.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analytical chemistry</subject><subject>Animals</subject><subject>Antioxidants</subject><subject>Cattle</subject><subject>Chromatography</subject><subject>Complexity</subject><subject>Fourier transforms</subject><subject>Free radicals</subject><subject>Identification</subject><subject>Lipid peroxidation</subject><subject>Mass spectrometry</subject><subject>Methionine - metabolism</subject><subject>Molecular Sequence Data</subject><subject>Multiple database searches</subject><subject>Nitrogen</subject><subject>Oxidation</subject><subject>Oxidation-Reduction</subject><subject>Oxygen</subject><subject>Peptide Hydrolases - chemistry</subject><subject>Peptide Hydrolases - metabolism</subject><subject>Peptides</subject><subject>Post-translation</subject><subject>Post-translational modifications</subject><subject>Proteases</subject><subject>Protein Processing, Post-Translational</subject><subject>Proteins</subject><subject>Proteolysis</subject><subject>Proteomics</subject><subject>Reactive nitrogen species</subject><subject>Reactive oxygen species</subject><subject>Scientific imaging</subject><subject>Trypsin</subject><subject>Ubiquitin</subject><subject>Ubiquitin - 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Irreversible oxidative PTMs can generate a complex distribution of modified protein molecules, recently termed as proteoforms. Using ubiquitin as a model system, we mapped oxidative modification sites using trypsin, Lys-C, and Glu-C peptides. Several M+16 Da proteoforms were detected as well as proteoforms that include other previously unidentified oxidative modifications. This work highlights the use of multiple protease digestions to give insights to the complexity of oxidative modifications possible in bottom-up analyses.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25775238</pmid><doi>10.1371/journal.pone.0116606</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Amino acids Analytical chemistry Animals Antioxidants Cattle Chromatography Complexity Fourier transforms Free radicals Identification Lipid peroxidation Mass spectrometry Methionine - metabolism Molecular Sequence Data Multiple database searches Nitrogen Oxidation Oxidation-Reduction Oxygen Peptide Hydrolases - chemistry Peptide Hydrolases - metabolism Peptides Post-translation Post-translational modifications Proteases Protein Processing, Post-Translational Proteins Proteolysis Proteomics Reactive nitrogen species Reactive oxygen species Scientific imaging Trypsin Ubiquitin Ubiquitin - metabolism |
| title | Multiple proteases to localize oxidation sites |
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