A filtered database search algorithm for endogenous serum protein carbonyl modifications in a mouse model of inflammation
| Autor: | Elizabeth M. Iffrig, Peter G. Slade, Alison Chiang, Steven R. Tannenbaum, John S. Wishnok, Michelle V. Williams |
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| Přispěvatelé: | Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Chemical Engineering, Tannenbaum, Steven Robert, Slade, Peter G., Williams, Michelle V., Chiang, Alison, Iffrig, Elizabeth, Wishnok, John S. |
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Technological Innovations and Resources
Protein Carbonylation Biotin Peptide Nitric Oxide Tandem mass spectrometry Biochemistry Analytical Chemistry Mice chemistry.chemical_compound Tandem Mass Spectrometry Cell Line Tumor Animals Database search engine Databases Protein Molecular Biology Inflammation chemistry.chemical_classification Chromatography biology Blood Proteins Avidin Blood proteins Disease Models Animal Oxidative Stress chemistry Biotinylation biology.protein Lipid Peroxidation Oxidation-Reduction Algorithm Algorithms Software Chromatography Liquid |
| Zdroj: | Prof. Tannenbaum via Howard Silver |
| Popis: | 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) |
| Databáze: | OpenAIRE |
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