A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation
During inflammation, the resulting oxidative stress can damage surrounding host tissue, forming protein-carbonyls. The SJL mouse is an experimental animal model used to assess in vivo toxicological responses to reactive oxygen and nitrogen species from inflammation. The goals of this study were to i...
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| Format: | Article |
| Language: | en_US |
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American Society for Biochemistry and Molecular Biology
2012
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| Online Access: | http://hdl.handle.net/1721.1/69076 https://orcid.org/0000-0002-2325-552X |
| _version_ | 1826189622928998400 |
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| author | Slade, Peter G. Williams, Michelle V. Chiang, Alison Iffrig, Elizabeth Tannenbaum, Steven Robert Wishnok, John S. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Slade, Peter G. Williams, Michelle V. Chiang, Alison Iffrig, Elizabeth Tannenbaum, Steven Robert Wishnok, John S. |
| author_sort | Slade, Peter G. |
| collection | MIT |
| description | During inflammation, the resulting oxidative stress can damage surrounding host tissue, forming protein-carbonyls. The SJL mouse is an experimental animal model used to assess in vivo toxicological responses to reactive oxygen and nitrogen species from inflammation. The goals of this study were to identify the major serum proteins modified with a carbonyl functionality and to identify the types of carbonyl adducts. To select for carbonyl-modified proteins, serum proteins were reacted with an aldehyde reactive probe that biotinylated the carbonyl modification. Modified proteins were enriched by avidin affinity and identified by two-dimensional liquid chromatography tandem MS. To identify the carbonyl modification, tryptic peptides from serum proteins were subjected to avidin affinity and the enriched modified peptides were analyzed by liquid chromatography tandem MS. It was noted that the aldehyde reactive probe tag created tag-specific fragment ions and neutral losses, and these extra features in the mass spectra inhibited identification of the modified peptides by database searching. To enhance the identification of carbonyl-modified peptides, a program was written that used the tag-specific fragment ions as a fingerprint (in silico filter program) and filtered the mass spectrometry data to highlight only modified peptides. A de novo-like database search algorithm was written (biotin peptide identification program) to identify the carbonyl-modified peptides. Although written specifically for our experiments, this software can be adapted to other modification and enrichment systems. Using these routines, a number of lipid peroxidation-derived protein carbonyls and direct side-chain oxidation proteins carbonyls were identified in SJL mouse serum. |
| first_indexed | 2024-09-23T08:18:32Z |
| format | Article |
| id | mit-1721.1/69076 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:18:32Z |
| publishDate | 2012 |
| publisher | American Society for Biochemistry and Molecular Biology |
| record_format | dspace |
| spelling | mit-1721.1/690762022-09-23T12:11:25Z A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation Slade, Peter G. Williams, Michelle V. Chiang, Alison Iffrig, Elizabeth Tannenbaum, Steven Robert Wishnok, John S. Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Chemical Engineering Tannenbaum, Steven Robert Tannenbaum, Steven Robert Slade, Peter G. Williams, Michelle V. Chiang, Alison Iffrig, Elizabeth Wishnok, John S. During inflammation, the resulting oxidative stress can damage surrounding host tissue, forming protein-carbonyls. The SJL mouse is an experimental animal model used to assess in vivo toxicological responses to reactive oxygen and nitrogen species from inflammation. The goals of this study were to identify the major serum proteins modified with a carbonyl functionality and to identify the types of carbonyl adducts. To select for carbonyl-modified proteins, serum proteins were reacted with an aldehyde reactive probe that biotinylated the carbonyl modification. Modified proteins were enriched by avidin affinity and identified by two-dimensional liquid chromatography tandem MS. To identify the carbonyl modification, tryptic peptides from serum proteins were subjected to avidin affinity and the enriched modified peptides were analyzed by liquid chromatography tandem MS. It was noted that the aldehyde reactive probe tag created tag-specific fragment ions and neutral losses, and these extra features in the mass spectra inhibited identification of the modified peptides by database searching. To enhance the identification of carbonyl-modified peptides, a program was written that used the tag-specific fragment ions as a fingerprint (in silico filter program) and filtered the mass spectrometry data to highlight only modified peptides. A de novo-like database search algorithm was written (biotin peptide identification program) to identify the carbonyl-modified peptides. Although written specifically for our experiments, this software can be adapted to other modification and enrichment systems. Using these routines, a number of lipid peroxidation-derived protein carbonyls and direct side-chain oxidation proteins carbonyls were identified in SJL mouse serum. National Institutes of Health (U.S.) (NCI Program Project Grant CA26731) Massachusetts Institute of Technology. Center for Environmental Health Sciences (NIEHS grant P30 ES002109) 2012-02-10T16:20:54Z 2012-02-10T16:20:54Z 2011-07 2011-06 Article http://purl.org/eprint/type/JournalArticle 1535-9476 1535-9484 http://hdl.handle.net/1721.1/69076 Slade, P. G. et al. “A Filtered Database Search Algorithm for Endogenous Serum Protein Carbonyl Modifications in a Mouse Model of Inflammation.” Molecular & Cellular Proteomics 10.10 (2011): M111.007658-M111.007658. https://orcid.org/0000-0002-2325-552X en_US http://dx.doi.org/10.1074/mcp.M111.007658 Molecular and Cellular Proteomics Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf American Society for Biochemistry and Molecular Biology Prof. Tannenbaum via Howard Silver |
| spellingShingle | Slade, Peter G. Williams, Michelle V. Chiang, Alison Iffrig, Elizabeth Tannenbaum, Steven Robert Wishnok, John S. A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title | A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title_full | A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title_fullStr | A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title_full_unstemmed | A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title_short | A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| title_sort | filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation |
| url | http://hdl.handle.net/1721.1/69076 https://orcid.org/0000-0002-2325-552X |
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