Dataset Information

Alkylation Damage by Lipid Electrophiles Targets Functional Protein Systems

ABSTRACT: These data correspond to "Alkylation Damage by Lipid Electrophiles Targets Functional Protein Systems," a paper from Codreanu, Liebler, et al, published at the journal _Molecular and Cellular Proteomics_ in 2013. Modifications also include: 4-hydroxynonenal (HNE) (UniMod #53), H(16) C(9) O(2), Monoisotopic mass 156.115030 4-Oxononenal (ONE) (UniMod #721), H(14) C(9) O(2), Monoisotopic mass 154.099380 Modifications may be observed in both reduced and oxidized forms (a mass shift of two Da).

INSTRUMENT(S): LTQ

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Daniel C. Liebler

PROVIDER: MSV000078490 | MassIVE | Mon Nov 18 14:22:00 GMT 2013

REPOSITORIES: MassIVE

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Alkylation damage by lipid electrophiles targets functional protein systems.

Codreanu Simona G SG Ullery Jody C JC Zhu Jing J Tallman Keri A KA Beavers William N WN Porter Ned A NA Marnett Lawrence J LJ Zhang Bing B Liebler Daniel C DC

Molecular & cellular proteomics : MCP 20140115 3

Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively acr ...[more]

PMID: 24429493

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Project description:We investigate molecular effects of glucosamine supplements, a popular safe alternative to non-steroidal anti-inflamatory drugs for decreasing pain, inflammation and keeping joints healthy. Numerous publications state an array of different molecular effects upon glucosamine treatment. We question whether these differences resulted mainly from focusing on a specific sub proteome or because different cell lines or tissues were used in the previous studies. To address this question global MS- and transcription array-based glucosamine drug profiling were performed on lymphocyte derived cell lines. We combined global label free MS-based protein quantitation with an open search strategy to obtain the best possible proteome coverage. Our result in large part support previous findings in a variety of cell models. Glucosamine induce O-GlcNAcylation but we also observe global changes in acetylation, methylation, phosphorylation. Furthermore, we mapped novel O-GlcNAc sites, on ER lumen proteins, regulated upon glucosamine treatment which provides novel insights into the role of glucosamine in ER stress. Preprocessing of MS data: All Q-Exactive data were calibrated using polycyclodi-methylsiloxane (PCMs—outgassed material from semiconductors) present in the ambient air and Bis(2-Ethylhexyl)(Phthalate) (DEHP—from plastic)1, 2 using both MaxQuant version 1.3.0.53 and modular VEMS mVEMS4. mVEMS4 further allows alternative parent ion annotations for each MS/MS spectrum which is needed if two peptide elution profiles overlap in the m/z and retention time dimension. By allowing alternative parent ion annotation for each MS/MS spectrum, provides a space efficient data format. Furthermore these alternative parent ion annotations were taken into account during the search. Database dependent search of MS data: All data were searched with MaxQuant version 1.3.0.53 and VEMS5. Mass accuracy was set to 10 ppm for peptides and 10 mDa for peptide fragments. Four missed cleavages were specified and the database UniProtKB/TrEMBL were used including permutated protein sequences, leaving Lys and Arg in place, together with common contaminants such as human keratins, bovine serum proteins and proteases6. Fixed modification of carbamidomethyl cysteine was included in the search parameters. In MaxQuant the following variable modifications were considered: Met-loss (UNIMOD 765), Oxidized methionine (UNIMOD 885), O-GlcNAc (HexNAc, UNIMOD 43). In VEMS a list of variable 36 modifications were considered for all data against the full protein database were performed. Protein N-terminal Met-loss is not in the list of VEMS modifications since VEMS by default always looks for N-terminal Met-loss. The modifications Phosphate-ribosylation (UNIMOD 1356), ADP ribose (UNIMOD 213), hydroxylation (UNIMOD 35) and Myristoylation (UNIMOD 45) were not frequent at a 1% FDR threshold and the search was therefore repeated excluding these modifications.

Dataset Information

Alkylation Damage by Lipid Electrophiles Targets Functional Protein Systems

Publications

Alkylation damage by lipid electrophiles targets functional protein systems.

Similar Datasets

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